Bass (LM and SM) wont hold on to feathers and fur like they do plastics, so knowing when the fly is in the fishes mouth, and having quick enough reflexes to get him stuck is the trick. The best way to know you've been bit sub-surface is to see it happen, try flies tied with a little bit of highly visable material (pink, chartruese, white, ect) and fish it in the zone where you can just barely keep an eye on it..... When the little pink, chartruese, or white light disappears, set the hook immediately.
An olive rabbit strip leech (unweighted or lightly weighted) with a collar of bright material makes a deadly sightfishing fly for smallies, as do muddlers with a white or chartruese head.
You may be getting tons of bites on those crawdad flies and such....but you'll only be aware of a small percentage of them if you can't see the fly. Because of what i call "the ol' Suck and Blow".
Even soft spun hair bugs like the one Ronnie posted wont get held onto like you'd expect...they'll rush over to it, suck it in...and blow it right back out, and this takes place in a half a mili-second unless BY CHANCE the hook momentarily hangs up on his lip as he's trying to expell it.