"Furthermore, if the US has them, will the Geneva Convention/US Army Field Guide be respected?"

If the US has the al Qaeda members, then there's two possibilities:

1. If the US admits that it has the al Qaeda personnel, then the legal niceties are likely to be observed regarding their treatment.

2. If the US does not admit that it has the al Qaeda personnel, then it's likely that the legal rights of the prisoners will not be respected.