Setting up 2 power amplifiers to setup at once help?

Might consider using the 2801 to power the highs for your speakers and the 'sub' out from the 2801 into the Yamaha to power the lows. 

Make sure there is no bridge between the speaker inputs. 
If you can dial in the crossover freq. start at lowest and move up to level that works. If not available set front speakers to "small" (which I would do anyway). 

"Imo, it's not a good idea, you don't want to use a active crossover in the receiver and the passive crossover in the speakers at the same time. "

I am curious why you think this. You are simply sending a signal that has passed a low-pass filter to another filter that should pass that signal (if set low enough). 

I can see a situation where the signal sent from the receiver is too 'low' for the difference between the frequency ranges of the low to mid speakers, which is why I advised to dial it up till it sounds full. seems like this method would allow you to better control the low end. 

On the other hand I see no issue with doing it like you suggested (as I have done both) except it is harder to control the 'amount' of low end. 

"So using the sub-out signal to drive the low frequency amplifier would cause frequencies between approximately 80 Hz and 125 Hz to be under-emphasized or even almost absent"

Good point, which is what I was trying to emphasize here-
"I can see a situation where the signal sent from the receiver is too 'low' for the difference between the frequency ranges of the low to mid speakers, which is why I advised to dial it up till it sounds full."

This is exactly why I didn't try it with my system since my stereo  crossovers are pre-selected at 60, 80 and 100 Hz and my speaker crossover is set to 125. I had thought an AVR would have a more flexible range. My mistake.