I only have two floor speakers, a center speaker, and a subwoofer. What setup would give me the best sound when connecting these to a 6.1 surround system. Just to head these comments off, I now the best way would be to purchase 3 more speakers but we are working on that and have to deal until we can buy the additional speakers.
It's basically the same setup as a 5.1 without the rear speakers. Set the output to stereo
Keep in mind that when you setup a Dolby Digital receiver, you select which speakers you have. So when you turn off the surround speakers in the speaker setup menu, the receiver will automatically adjust the sound accordingly. Modern receivers have been programmed to understand missing speakers vs. all being installed and takes that into account.
You failed to mention what AV Receiver you are using, or what make model speakers you have. These are NOT the left over speakers from some crappy $399 box system - are they? You cannot use these on other gear. Basically - you just wire up the sub and 3 front speakers and ignore that you do not have rear sounds. If you have not purchased an AV Receiver yet - the Yamaha RXV-6 series has a nice feature. You can tell the receiver you have hooked up 1 speaker and it will route all the sounds to that single speaker. Or you can use 2,3 or 5 speakers and it will adapt. Hope this helps.