EasyTutu creates a separate installation for you to enjoy, but only for the BG1 part of the game. For BG2, you have to create a separate installation and import your character(or your saved game) from EasyTutu. All BG1 mods(like BG1 NPC or BG1 UB) for Tutu go to EasyTutu folder, all BG2 mods(like Quest Pack and Banter Pack) go to BG2 folder. If you want to install a mod that works for both games(Level 1 NPCs or BG2 Tweaks), you have to install it into both folders.
This way you'll have to have two separate installations for two different games, but there is a bright side: since the games are separate, there are fewer mods installed in total and the risk of crashing/lags/slowing your game is minimized.