DO NOT use them together! Isotrex gel is sort of a chemical exfoliant (but better) in the way that it speeds up how fast your skin cells turn over. Differin does the same thing but its basically less effective. So there's no point in using the differin aswell. The isotrex gel on its own will dry your skin out quite a bit at first, so the differin will only make the irritation worse.
Isotrex tends to make some people break out more at first, this is called 'purging' (like the new movie lol) where all of the potential spots turn into spots as your skin gets cleared out. To minimize this, take the antibiotics for 3/4 weeks before you start using the Isotrex and it should be a bit more forgiving on your skin.
Let us know how it works for you