OK, so...I think I know what I did that one time...
If you "record enable" the audio track for your guitar first, (set all your input monitoring and whatever else you want to set up).
Then, select the instrument track that has the BIAB plugin on it, load your BIAB song and set the plugin to follow Garageband (by double clicking plugin master track button).
Now without clicking on the audio guitar track, you can hit the big red record button on the top toolbar.
You will be able to record the guitar audio track in the background, while the BIAB plugin window is still in front.
I think that's what I did when I got it to work that first time.
Unfortunately, as soon as you hit stop it disappears again though.
But at least you can follow along while it's playing.
Hopefully this helps !
- Jay