If you're pretty familiar with how a Stratocaster and a Les Paul sound, you can tell the two players apart by their tone. The tone of Clapton's strat is thinner and pluckier. Also, I'm pretty sure that Duane Allman played all the slide, so if you hear slide, it's Duane.
One more thing to consider: if there are multiple guitar players, it's kind of a recording convention to keep them panned to the same side of the stereo image throughout an album. So if, in one song, you've identified Clapton coming out of the right speaker and Duane coming out of the left speaker, then on the other songs it'll probably be the same players on the same sides (I'm not positive this is the way it is on the Layla album, though).
I agree with others that Duane probably played the tastiest licks on that album. I'm pretty sure goosebump-raising outro solo on Layla is all Duane. On the other hand, Clapton's solos on Bell Bottom Blues are really pretty, and he positively burns it up on Have You Ever Loved a Woman. I guess I'd call it a draw.