There are persons who are able to keep their living and working places tidy, even though they constantly use them. They seem to have automatized basic tasks that are needed to do between your work such that the tidiness is kept.
I am not one of these persons. When I use space, this space gets untidy. Sitting somewhere, working at something, scribbling a note and then just dropping it when not needed anymore is far easier than locating a bin and actually putting it there. Context switches are productivity killers.
However, with this kind of behavior, the room gets untidier, and you regularily need some time to tidy it up again. Depending on my mood, I do this more or less often. However, it is rather hard to have an objective discussion with people about why I do not immediately tidy up everything.
As with so many current topics, the problem lies in "moral" views rather than rational considerations. It is basically the common opinion that a room has to be tidied up. If you do not keep your room tidy, your mind is not tidy, and if your mind is not tidy, you are not effective and will not achieve as much as a tidy person - that is the general opinion. And of course, the order of utilities can make them easier to find and might therefore increase efficiency. However, there are some very successful people who are rather chaotic than tidy. A famous Einstein-quote in that context is, for exampleIf a cluttered desk signs a cluttered mind, Of what, then, is an empty desk a sign?
Another thing is that chaos can also be productive. Penicillin, for example, was discovered by a contaminated petri dish.
I do not claim that cleaning up is useless in general - it is necessary to clean and tidy things up from time to time. And if you are sick, for example allergical, it is necessary to clean up regularily. But if there is no special reason, be brave and look how things are getting untidy.
Some people claim that one feels better in a cleaned room. This might be the case for some people, but on the other hand, a room that is tidied up completely often feels empty and lifeless. To prevent this, the people buy ornamentations and staubfangers. Well, I feel better when the things in my room are arranged symmetrically, but I admit that this is a spleen, I do not use it as an argument for others to arrange their stuff symmetrically. So tidying up just for the sake of tidiness is a part of our culture, nothing more.
Especially, a common misconception sees tidiness as something that can be achieved and then stays where it is until it is broken by something intrinsically bad. This is wrong. Tidiness is a product of maintenance, not an achievable state.
Now, assuming you actually want to tidy up your room, which is - as I said - a good thing if it is done wisely and not just for its own sake, there are a few things to consider.
Firstly, tidying up decreases the entropy, while nature usually tries to increase the entropy. That means that the universe will do everything it can to keep your room untidy - always keep that in mind. It is natural for stuff to get messed up, to prevent peaks of energy. But on the other hand, minimizing the amount of energy peaks will also put a structure onto your stuff. For example, you yourself are a peak of energy, and having stuff you often access far away from you increases this stuff's energy. Usually, the items you often use are near the places you use them, except maybe for special reasons like keeping your keyboard away from your tumbler. Often, dirty stuff groups up, and keeps separated from clean stuff. And furthermore, big stuff will be surrounded by smaller stuff: big items do usually not form groups and will drift away from one another, keeping "clouds" of smaller stuff around them.
Look at your room when it is messed up. I am sure you will see some of this. Of course, you are a self-aware being, and this look on mess produced by you is not always accurate, but it is what I have seen in many untidy rooms. It seems to be the "natural order" of stuff when used while not being tidied up, it is a form of self-organization.
The important thing to keep in mind when tidying up is that self-organizing systems are often locally optimal, that is, sufficiently small changes will make it worse, and "sufficiently small" can still be pretty large. Usually, it goes like this: You tidy up a part of the stuff you have, you find more stuff to tidy up, so you tidy it up, just to find even more stuff to tidy up. A metaphorical "fractal" of mess, sort of. Make up your mind about the scale you want to tidy up. If you are sorting your crayons while your dustbunnies gain self-awareness, you do something wrong.
If you really want to tidy up, you need to replace the natural order by a good artificial order. The natural order can give you clues for that.
Items you often use will find their way back to you soon or later. If you want to prevent them from lying about on the floor again, put them somwhere you can easily reach them and easily put them back.
In case you find something buried under a lot of other stuff, think about whether you really need it. If you do not need it, throw it away, give it away, sell it on ebay or donate it, depending on what it is. If it has an intrinsic value for you, at least put it out of your way: Use it for decoration at some place you do not need, or put it in a box into your attic. Otherwise, you will burry it again, anyway.
Did something fall on the floor or tilt over? That means that the state in which it was in the first place was unstable. Think about keeping it where it is now - it found its way to its place automatically, so at least think of a reason to force it to somewhere else. Of course, if it is garbage, throw it away!
Keep in mind that your brain uses "anchors" for its daily tasks, like an item that reminds you of buying food, or an item that just reminds your subconciousness to produce endorphines. Anchors you might not be aware of before they are gone. Especially when cleaning up after a long period, these anchors might get lost, and with them an important mechanism for organizing your life. Be aware of this.
Furthermore, even though it sounds unplausible, for more than one time I expierienced that stuff gets lost after cleaning up, especially items which are used seldom. If you have a screwdriver to bleed your heater which usually lies on your desk, and you decide to put it somewhere else because you do not need it often and it looks untidy on your desk, chances are that you will forget where you put it, but still remember that it used to be on your desk. Think about whether you really have to put such items away. In many cases, it is the best to just leave them where they are.
Now that you have made up your mind what you want to place somewhere else, some people suggest you to have some sort of register for your stuff, especially paper-stuff. My expierience is that such registers tend to become overful and unusable. Sure, a lot of important stuff is at the same place, but what is the "inner" order you give it? Often, there is a lot of small crap you have to keep that has no particular obvious order, and thus will always remain unsorted. A chaotic drawer can be better than a highly organized register, depending on the amount of stuff you have. It is better to have a compromise: Use drawers for major topics, for example, "Work", "Finance", "Health", "Electronic Devices", etc. - you can of course use registers for it, but it is a pure waste of time to try to keep any order into these. Just put stuff into there and throw away stuff you find that you do not need anymore and put it into some cabinet.
Also many paper sheets you have are not needed in original. If you have a scanner, digitalize them and save them on some backup device (be careful to use a proper backup system, though). It needs less place and is easier to search through.
To achieve the best results, try to keep in mind that your aim is not to tidy up your room at first place, but to make it look tidy. Try to create huge plain areas - start at the center of your room, rather than at the edges. Try to create a "bubble" of tidyness. A few items lying at the side of your room will look ok, and if they really annoy you, just put them in your wardrobe, where nobody sees them.
Stuff underlies "diffusion": It will find its way into every gap. That is, try to block the common gaps, like under your bed, or under chairs, or behind your wardrobe, maybe by some items that fill up that place. For example, under your bed, there is a good place for suitcases.
Let us assume you are almost done, and now have a lot of stuff which you want to put in some junk room. Of course, your chair is so comfortable now, and you are so exhausted from tidying up, that you will not do that right now. You will likely just forget it, keeping it in your room, burying it with new stuff until the next time you clean up. The best way to prevent this is to put the stuff somehwere it annoys you, for example, in front of the door, or in front of your bed. It must get on your nerves so much that you cannot get used to it. Then you will find a moment of free time when it annoyes you so much that you will put it away - well, at least with a higher probability.