The surrounds at 90 or 100 Hz should not matter. Not much bass there anyway.

I will second the idea to put the sub a corner behind the mains. Then let Audyssey do its thing.

Also, when using Audyssey, check out the guide over at AVS forums. There are many things you can do to get poor results. The manual that comes with the AVR is to basic.

Dave
Audyssey Setup Guide