Can I use the auto set up to allow the 990 to figure out the distance from the main listening position and the speakers, and then when auto set up is complete go back and adjust the cross overs without whiping out the the other settings?
Absolutely. Once it's done it has no influence over the settings
I can not find the documentation that came with the speakers any where so I don't know excactly the limit of their proported frequency response. Any way that can be measured? Does Radio Shack sell something along that line, or am I going to need a little trial and error to find what I like the best.
In theory, you could use Room EQ Wizard (a free program) and a Radio Shack SPL meter to calculate the response of each speaker, but that's going to be a somewhat tedious exercise. Trial and error is also an option: start at an 80Hz crossover and tinker with it.