http://digital.library.okstate.edu/kappler/Vol2/Toc.htm
and scroll down to "Comanche". The first treaty between the US government and the Comanche didn't occur until 1835. Two first cousins of one of my great great grandma's were stationed at Fort Gibson in 1832, so they "might have been" on the expedition that made first contact with the Comanche, Kiowa and Wichita in 1834, so I have read up on this first treaty. This meeting took place because of an Osage massacre of a Kiowa Village in the Wichita Mountains of SW Ok. a couple of years earlier. The next treaty was in 1846, and the next 1853.
http://digital.library.okstate.edu/kappler/Vol2/treaties/com0892.htm
This (link above) treaty is the first that lists the boundaries (article 2) of the Comanche Nation, and it is dated 1865-66. I did not see the name of the Confederate Comanche listed as a signer of that treaty. Nothing about the Civil War is mentioned, even though the timing of the treaty (1865-1866). suggests that possibility. They are given lands formerly given to the Chickasaw/Choctaw. Not all the Comanches move to this land immediately. I find it difficult to believe they cared one way or the other who won the Civil War. They were a warrior culture, and would fight anyone trespassing on their lands, Confederate or Union. One Comanche Chief might have signed a treaty saying he wouldn't raid Texas or the Chickasaw -- but I bet as far as they were concerned, chiefs of other Comanche bands were not bound to leave Texans alone. As always, I reserve the right to be wrong . . . :)
http://digital.library.okstate.edu/kappler/Vol2/treaties/kio0977.htm#mn6
same -- article 2 lists boundary on Indian lands. Treaty dated 1867-68. No mention of the Civil War. The last Comanche moved to their reservation lands in 1875.