What condition are your cards in?
First of all, I store in these boxes. They are sorted by set in there so there is some moving them around as I add new ones or remove old ones.
The good stuff goes straight into toploaders. They will be on the good stuff list. Otherwise, everything will be loose but well taken care of except as noted in the list.
I also keep some in binders. These are mostly for complete sets but there are some extras/dupes in binders as well for the boy to take along to friends houses to trade.