To the oringal questions asked by the OP I sort by sport, then move them into manufactures (Topps, Panini, UD, Fleer, etc.) going by the trademark on the back. Then I sort each set into sets with duplicates added in. I upload each card from highest to lowest, removing duplicates as I go. If I have a complete set then I move it into a binder. If I do not then I put it back into the box with other sets from the same manufacure and label that on the side of the box. The duplicates are all put into a 5k box that is used for trades.
When life has you down buy a pack of cards and realize you overpaid.