I see. I keep all of my mine decks separate. Easier to search for tiles that way. At the beginning of each mission, we draw a world card to determine which mine deck we are using, this way we only ever need to search through one set of tiles.
I'll just insert the 6 passage cards from another deck when the Derelict Ship is chosen.
I have mixed all minecards from all three of my expansions together, but I don't search for maptiles either. Every minecard is marked with a letter and number, every maptile with the corresponding letter and number. Then I have them sorted in a file carrier with two maptiles per pocket. Easy setup.