The Mod manager you downloaded was most likely the Fallout 3 mod manager, it's called FOMM for freaks sake, and started by running the fomm.exe.... not the discontinued BG2 Multi install tool. Read the origin thread again and you are likely to discover this to be the factual case.
The best thing you can do is copy the current game folder to a safe space, "uninstall" the game using the Control Panel and removing the game folder and then reinstall it to the same folder, then cut the new games folder to elsewhere and then cut paste the old game folder to where it originally was, then edit the new folder's baldur.ini file's [Alias] directories so it's in the new locations.
Now to the kits, you need to install them to the game folder you wish them to be in, so in a Tutu game, you first need to have a clean BG1 and BG2 installs, then make the EasyTutu install that creates a new game folder, then you should of course start it and a new game in it so you can see if there's things you need to adjust(black boxes etc.) Then you can modify it further, and install the megamodkits mod to that folder.
Edited by The Imp, 31 January 2014 - 04:02 AM.
Yep, Jarno Mikkola. my Mega Mod FAQ. Use of the BWS, and how to use it(scroll down that post a bit).
OK, desert dweller, welcome to the sanity, you are free to search for the limit, it's out there, we drew it in the sand. Ouh, actually it was still snow then.. but anyways.
