The auto setup part sets the delay(distance), levels (dB of each speaker), and checks polarity (makes sure you hooked the wires up right. Distance can be done with a tape measure to the main listening position. Levels can be done with the receiver test tones and SPL meter from Radio Shack, or if your real good, you can do it by ear. I hope you can hook up the speaker wires.
As far as the sub, the autosetup does ok, but it would be best to use a meter.
The Room EQ stuff I would leave off.
Which sub do you have? We can help you with the volume on the sub versus receiver, and crossover setting on both, this is important.
What a heck of a wife you have man, mine got me a 2805