How do you store/find your cards that are in multiple sets?

[AMBST95]

I was looking through the archive section tonight trying to get some ideas, but wanted to try to get some fresh feedback. I apologize in advance if this has been rehashed too often. Here's my question. As my collection is getting larger, I have more cards that are a part of multiple sets that I am working on. For example, I have a T206 Cobb that I count toward my T206 company set, my HOF player set, and a Cobb player set. I have always stored the players sets as groups seperate from the company sets, but finding cards to share and look at is becoming more of a hassle as my collection grows and new sets are created. What do you do when your collection becomes so unwieldy? Should I just give in to photobucket albums to view my player/company sets and store the cards in chronological order to avoid the confusion? I don't want to lose track of where things are, but I enjoy being able to look through my cards as the groups they've been collected as. Does anyone use place markers (ie - This card is on loan to the Cobb set) or am I setting myself up for more headaches down the road by keeping the player sets stored separately? I would love to hear your ideas, especially from those with both player and company sets.