Glancing at your manual I don't see a setup suggestion for 6.1, nor much explanation of the sound modes at all. Seems to me on my avrs that do specify 6.1 with the single back surround the left back surround was the usual connection method. In your case I'd simply run MCACC as is and let the avr do it's thing....if it sounds wrong disconnect the back surround and rerun MCACC....
I did find more info I can share. The Advanced Manual for the Pioneer SVX-1131 can be found here:
http://intl.pioneer-audiovisual.com/manuals/docs/SN29402388_604.pdf
On page 9 it has the different speaker configurations:
Default value: 7.1.2 ch
Options: Select "2.1 ch", "3.1 ch", "4.1 ch", "5.1 ch", "6.1 ch",
"7.1 ch", "2.1.2 ch", "3.1.2 ch", "4.1.2 ch", "5.1.2
ch", "6.1.2 ch", or "7.1.2 ch" to suit
When you select 6.1 you cannot use the Center speaker. You have to select 7.1, then run MCACC. It will detect that you only have one Surround Back speaker (L or R), like in my case, and make the sound adjustments.
Note: You cannot use the Zone 2 with this setting. It has to be a 5.1 or less configuration as the Zone 2 connectors are the same as the Surround Back connectors. Speaker B is on this unit is designed for Front Height speakers or similar, you cannot control Speaker B from your remote or app.
I have opted to use my older AV Receiver to drive my patio speakers with it.