As someone who is not overly organized and with a great many magic the gathering cards I have spent many hours trying to get them organized and never fully succeeded but I have learned enough that I can usually find the card that I want reasonably fast, so long as it is where it is supposed to be.
The first thing I would suggest is to get two three ring binder with the plastic sleeves for cards. Do not try to put all of your cards in this though, if you play for any period of time you are going to run out of room. The first of these binders is for your tier one cards, the ones which will go into nearly every deck of their color. Things like wrath of god, birds of paradise and dual lands. This will be the first place you search when you are building a deck and while the specific cards may change the core of it is likely to stay the same.
The second binder is a trading binder. This is where I put any good card that I have more than four of, or cards that are valuable but you don't care all that much about. The value of this is that you have a binder people who want to trade can look through. Both of these binders should be organized by color, but there are few enough cards that they probably don't need to be much more than that.
Next I would suggest a box big enough to hold a single row of about a thousand cards. This will be enough for a while but its true purpose is to keep the cards that are tier two. Cards which go in specific types of decks. Gold cards that are very good, Llanawar Elves, and Shivan dragons, all of which may go into your deck, but you don't need to look at every time. This is also a good place to keep extra basic land, as this will be the box you want to take with you when you go places. The reason for this is that it is far easier to ask the people at the game store to put a small box behind the counter and then you don't have to watch it.
Finally as your collection grows you will want to buy a larger box. Most of these boxes have five rows, if you can find one with six that is ideal though. The obvious place to begin is by color. This is where you will but most of your commons and uncommons. If you do want to sort beyond color I suggest by set as this makes it far easier to build by specific format.
Finally if you've done all that and you want to continue buying the small cheep plastic sleeves that seem just a little to big for magic cards are a good way to group cards in to small sets as you can usually fit four cards into it without too much cramming. This will make it far easier when building a deck because once you've found the cards you have found all four.