Well, you start the game from where you modified it... this usually is strait forward as you don't use a mod manager to download and extract and install the mods, but do that yourself and learn that the game is where it is. Mostlikely, you should start it via the BG2EE's Baldur.exe file. This is unless you chose the EET's make new game in a new folder option, if it has it... this depends on how exactly deep you dwelved into the moding and how you chose the options you did. But you should know what each of them do before you choose ...
I understand your point. The real issue is that I see different mods and installs both in BG1 file and BG2 file, so it brought to me the question: if I play BG2Trilogy (through BG2EE's Baldur.exe file as you mentioned), will I enjoy the mods installed in BG1 file? Thank you.
Well, yes, in case you used the EET to the BG2EE to bring the two games together, as it brings all the data from the BG1EE to the BG2EE, and does some small conversion to keep things nice, which is why the install needs that much space. But you can uninstall the BG1EE...
This is similar to what the BGT-weidu did... just with the exception that the BG1 needed to be clean install and the mods needed to be then BGT compatible to bring any changes made to the BG1 portion into the BG2 game... in the non-EE version of the games.
if I play BG2Trilogy
1 thing I request: Learn from this experience, never ever use that again, cause it will either bring confusion or recentment from everyside.. as there is the EET, aka Enhanced Edition Trilogy, and the other is the Baldur's Gate Trilogy, later adopted to -weidu mod ... aka; BGT-weidu ... and there was actually 4 parts of it, and now the EET has 5.. but never that be minded.
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.