Theoretically this should work, I only have 1 monitor so I can't test it myself.. but try this:
pre-requisite: you'll need to be using one of the DX9 blitters for this. (IIRC)
Select "Video -> Choose Fullscreen monitor", and select your second monitor for both pulldowns
Toggle on "Video -> Auto switch to fullscreen after loading"
start FBAlpha on first monitor.
best regards,
- dink