Nothing I changed in /usr/share/pulseaudio/alsa-mixer/profile-sets/default.conf (or any single conf file I changed) did anything to show another order in paman or to play sounds on the center and subwoofer properly.
However, I did get the channel map order to show lfe and center the opposite way by specifying a remap and attaching it.
load-module module-remap-sink sink_name=lfe_center_swap channel_map=front-left,front-right,rear-left,rear-right,lfe,front-center
default-sample-channels = 6
default-sink = lfe_center_swap
That didn't fix the reversed sub/center problem either though. The paman volume control display shows the same thing and the sounds are the same even with the order reversed. 4 (center) shows something is playing but both the subwoofer and center speaker are silent. 5 (lfe) shows something is playing, which the center channel plays. So it's still backwards. That's when playing a file (such as Nums_5dot1_24_48000 from here) or when using speaker-test -c6 or by switching mixers or players.
This is an Asus P5LD2-VM DH motherboard using the ALC882 with the outputs Gray Black Orange Pink Green Blue (side, rear, sub/center, mic, front, line-in), It goes to a 5.1 speaker system with black-rear orange-sub/center green-front. (In the Offspring of Gates the sub/center sounds are also backwards -- but the Windows Realtek program has a check box to swap the output, and when that's checked, the output is proper.)
Perhaps somebody has a way to do the same thing in Ubuntu 12.04. But for now the answer is it doesn't work, at least not on my setup, even with the order changed in the channel map.