Well, I dont' believe you have to point towards specific files, the contents of mine is:
[Alias]
HD0:=d:\games\BGII - SoA\
CD1:=d:\games\BGII - SoA\CD1\
CD2:=d:\games\BGII - SoA\CD2\;d:\games\BGII - SoA\CD2\
CD3:=d:\games\BGII - SoA\CD3\
CD4:=d:\games\BGII - SoA\CD4\
CD5:=d:\games\BGII - SoA\CD5\
I think CD2 is an accident (the address repeated) but that's how it was in my file, so you can always take it out.
You were right to ignore the advice to dump all the contents of the CD folders in your main folder, the .bif files in each folder (CD2, CD3 etc) have the same names and would be overwritten.
I'm not 100% sure of what you're asking, but if you want the whole file, follow this link:
http://colin.htid.net/baldur.ini
Hope that's of some use..