Can I use 2 two channel amps to run a 3 channel system? leaving one side of an amp unused

What will you do with the unused stereo channel? Yes, a dummy load is the solution, but you'll be missing out on the full audio mix.

A possible setup could be:
Amp 1... L R 
Amp 2... sum the 2 channels to the middle speaker.

Any thoughts?

If the signal is a center channel output from a AVR wouldn't it be summed? 

The signal will be for a center channel from an AVR. Wouldn't the summed power be too much to the center?

If a tube amp you might be able to remove the input tube of the unused channel- that would remove the need for a dummy load at the output (which is not needed on all tube amps BTW). You might also be able to remove the output tubes of that channel as well- but in this regard I would check with the manufacturer.

The amp is a bel canto ref500s.