I tended not to be very organised with stuff put into boxes more or less by expansion.
I tried different methods and at the beginning had 4 of each cards (if possible) in binders of the respective color (yes even commons).
Then I had to move, leaving most of my collection behind (around destiny), selected only the mostly used commons/ uncommons but all the rares and took them with me (the rest is still waiting there ..)
Then around destiny it was the above mentioned method of boxes by expansion. Then I lost 2 masticores. Swearing that it would never happen again, and having less and less time to play and construct decks (ahh the joys of having a 50 hrs/week job and being married) I took the following initiatives, sorting methods and rules :
1) keep no more of 6 copies of each common / uncommon that will probably NOT see play. Keep plenty of copies of the GOOD commons (e.g. llanowar elves, rancor etc ...)
2) regularily (once ever quarter at least) check the ordonance.
Binders :
I try to complete each set and put them into binders by block. E.g Saga, legacy and destiny together. 1 card of each if possible.
I use those binders when I do deck building.
I have 1 trade binder with crappy and good rares, good uncommons.
And 1 binder for the stuff I DONT WANT TO TRADE unless .. In there you find the dual lands, moxes, etc, with 3 or 4 copies max of each. (no I dont have any 3 copies of the original moxes ... )
Boxes :
The white - carton like boxes are used with 1 for each expansion. They stay clean and tidy as I only remove the cards I will take to put into a deck after looking for them in the respective binders.
I keep 1 box for the "need to be sorted out cards" when I make my quarterly clean up.
Theme boxes :
I have 1 of those small transparent boxes for each color, land and artefact. In there go the cards that usually jump in and out of decks, like wall of blossom, armaggedons, soul warden etc.
When the boxes become full it is time to do some srting out.
"Starter" boxes for sealed play (I think you know what I mean, those packs with 75 cards and lands). In those I do have decks under construction and "themes" like blue control (all my counters and stuff), WW (disenchant) elves (all the elves that make it out of the boxes), slivers etc....
AND LAST BUT NOT LEAST, Deck boxes.
individual boxes for the archetypes, WW and suicide black.
1 anthology box with the "current" decks.
BTW the trading binder is organised as follow :
first 2 pages : the real good stuff (living death, fork etc...)
Then current type 2
lands/artefact/WUBRG
Then the rest
lands/artefacts/WUBRG.
The best advice is to try to find a method that works for YOU, where you can find the crads that you need quickly, and put them back.
Separate the stuff that u dont want to trade from the stuff you want to trade or in a stupid moment you will trade what you didnt want to trade.
Keep the "precious stuff" in those small plastic boxes or binders.
Enjoy yourselves ...
BTW, honestly, how many cards to you think you have ???
I guess I must have around 8000 .... DDDDUUUUUHHHH
way too many