I assume that you're using Audyssey. If so, there shouldn't be any issue.
When I set up my Onkyo 5508 (a near twin of the 80.2) I found that Audyssey would auto detect the set-up. It asks you to identify the sub or subs, then pings each of the other potential (side, rear, height, etc.) channels for level set and EQ. When the test mic produces zero response to the set-up ping for any given channel, Audyssey assumes that there are no speakers active for that channel. At the end of the process, it will show 2.2 for left/right with two subs or 2.1 for left/right with one sub.
Marty
When I set up my Onkyo 5508 (a near twin of the 80.2) I found that Audyssey would auto detect the set-up. It asks you to identify the sub or subs, then pings each of the other potential (side, rear, height, etc.) channels for level set and EQ. When the test mic produces zero response to the set-up ping for any given channel, Audyssey assumes that there are no speakers active for that channel. At the end of the process, it will show 2.2 for left/right with two subs or 2.1 for left/right with one sub.
Marty