OK. I installed into the SoA folder. TobExLoader works now but when BG opens up it's in a small square in the middle of my screen, off centre so I can only see about a quarter of what I am supposed to see, and the colours are all wrong. I've tried running it as an admin, in compatibility mode for Win95, 256 colours enabled, nothing's helped.
I've also tried running BG2 from the desktop shortcut but the same problem arises. But when running the BG1 shortcut the game plays normally but completely un-modded.