No problem, but you'll need to make sure you are using a mode which takes the stereo signal from the radio and expands it out to a 5 channel signal to make all the speakers work.
Something like Dolby Pro Logic II would do.
Alternatively, you could start at the speakers and work back. Look in the manual for test tones and push whatever buttons you need to get the test tones running. That will put a "shhh" pink noise signal out on one speaker at a time and let you verify that the speakers are all hooked up properly and the amplifier channels are all working.
EDIT -- if you haven't already read this article from Alan, it's worth a quick look. Bottom line is that the problems you are having are really common... a whole bunch of things have to be set correctly to get 5.1 out, and if ANY of them are wrong you're only gonna get stereo until you find the right setting.
Just keep telling us what you did and we'll get you through it...
... or just give the Axiom folks a call in the morning, they deal with this all the time as well. Home theater is like any other "open system" -- sure you get to mix and match, but you also need a room full of geeks to get the mix & matched system to work