I mainly installed the ones from the === BG2 === section here, following the suggestions on what to install or not:
http://www.gog.com/en/forum/baldurs_gate_series/newbie_guide_modding_bg1_if_you_buy_bg1_bg2_from_gog As for installing mods, part of the installation is done through the command line, and crossover doesn't seem to handle it that well, as it doesn't show it after the windows install part is done.
So, just run the mod installer normally (i.e. double click, and let crossover do the rest. This works fine). After the windows part is done installing, the crossover window will remain disabled. I believe this is because it is running the command line part in the background, but just not showing it. You can safely close this window.
Now, start a new execute window command (Programs -> Execute command) and in the command part write: wineconsole cmd
Make sure you have the bottle where you installed baldur's gate selected. This will open a terminal window on Z:. This is implemented by wine, and is somewhat rudimentary (there's no TAB completion of what you are writing), but works fine for this. It is also case insensitive, so don't worry with capital letter.
First go to C:
C:
Then navigate to the baldur's gate folder:
cd C:\Program Files\GOG.com\Baldurs Gate II
Now, you can view the command line executables for your installed mods:
dir *.exe
So, you just need to run them now, and follow the on screen instructions. I only installed 3 mods, so I had (along with the normal game exes):
setup-bg2fixpack.exe
SETUP-UB.exe
setup-widescreen.exe
As for the game, mine sometimes starts with a black bar on the bottom (the same height as the dock). I think selecting any window (e.g. a browser) after running BG2, but before it starts will usually prevent this from happening.
That should be it. If you find some of the instructions confusing, or have other questions feel free to ask.