I am having problems recording BIAB, unless I use an external mic and would appreciate any suggestions.

I use an iMac for BIAB (and everything else) and an Apogee Duet to plug in my guitar. When I try to record a clip using Photo Booth, I get my guitar (in one channel) but not the BIAB track. I've got the Duet setup for input and output, and I get the backing track through it without problems. However, nothing comes out on the Photo Booth recording (unless I use an external mic and record through the speakers).

Thanks for any help / suggestions.