I do what Blargney and Dave do... I keep each set in a small clear plastic, snap lid container. I prep before the game using large zip Ziploc bags for rooms/common areas. I also have resin barrels from Remax Village, Dwarven Forge, crates, and so forth... sometimes I lay out the dungeon first and uncover it as they go, other times I assemble it as I need to. Within a few games, I got familiar with the sets, and although I really don't care yet for the Caverns of the Underdark, I love the rest. I order generally 3 sets each time, although I got 5 of Streets.. because I can set up a few blocks of a town.
I don't know if you've ever gone to look in the aquarium props section of major pet stores, but I have some incredibly cool ruined archways, pillars, tree stumps, fallen logs... which make my 2D tiles come alive with minor dressings and enhancements. My players love them, and once I used them a little, I am very familiar with them.
I keep small boxes or bags of special tiles, like braziers, holy water fonts, trapdoors, ladders, and I do keep all my stairs, chairs & tables, and like bookcase/carpets/pews aside.
I NEVER knew they were dry erase after using them for years, and I can't wait to try them tonite!