Audyssey's subEQ is excellent IMO, however the rest of the RC (XT32) is mostly personal preference. Some people love it, some people hate it. What XT32 and the rest of the audyssey lineup does pretty well is set the delay among a few other things. If you plan on running 2 subs, but don't want to invest in some more equipment to get some equalization to your subs then yes it is definitely worth it.
Proper placement and setting the distances might get you close, but you won't really know for sure (except by ear) unless you get a measurement mic and download REW. The other issue is that when audyssey sets the distance it is also accounting for any signal delay that is needed, which it sounds like you're not taking into account. It's tough to say how much EQ you really need without a measurement mic at minimum (or SPL meter) and REW).
So to sum that up, XT32 can be hit or miss depending on your tastes, subEQ is almost always a winner. Problem is you can't have one without the other. Proper placement may get you close, but it's impossible to know for sure and by how much without making a smallish investment in some measurement gear.