Spells & Rooms get shuffled together in one big deck. And we mix the bosses of both versions in one deck to draw from. But we draw two and choose one for personal preferences.
Just to be clear, Spells and Rooms should be in *separate* decks. One deck for Spells and one deck for Rooms. That is probably what korneeltroch intended to say, but didn't want anyone to come along and be more confused.
You can mix and match Boss Monster 1 and 2 cards as you see fit. Either giant piles or take whatever cards you like from either set and create decks. The two sets are very compatible. I found that they play rather well off of each other if you do mix them.