as your collection grows, so must your storage solutions change. Here are the phases my collection went through:
phase 1: everything stored randomly in prerelease and bundle boxes
phase 2: buying a few empty bundle boxes online so I have 5 bundle boxes, storing per colour and in ascending mana value
phase 3: getting a longbox (google 'tcg longbox') that holds 1000 cards and storing my cards in there. At this point I switched to ordering in the objectively best way for big collections: per set, from oldest set to newest set, in ascending collection number (the number on the bottom left of the card). Ordering per collection number will also automatically order your cards per colour and alphabetically for every set.
phase 4: getting multiple longboxes to accommodate the ever expanding collection, continuing with the collection method of phase 3
trades are still in a binder though!