I picked up a couple of guys who are terrific pass rushers, but not-so-great at everything else, thinking "hey, they're good for 3rd & long". I've got a 3rd TE who isn't much of a pass-catcher, but he's a crushing run-blocker for short-yardage situations. Question: Will the computer actually sub these guys in when it makes sense?

u need to sub them in using overrides. You can put them in on short yardage downs in specific formations. It's on the depth chart page

Or in the pass rushers' case, perhaps, be tactful and match-up lets say Nickel blitzes (plays) and the formation in the over-rides to slide these guys in there for the extra oomph.