It's definitely a good idea to keep the ratings separate. They're two different games. However, I was surprised to note that my seek for my first 960 game required me to include my "rating" in the range of possible opponents - by which it meant my normal chess rating of 1618, not my 960 default rating of 1200.
Chess960 RATINGS

960 has its own rating. The points awarded are not influenced by an opponents online chess rating. It doesn't matter that someone is higher rated and therefore "better" in standard chess, because they might totally suck at 960.
i don't necessarily think this is true, but i do think that the ratings have to be seperate, and there wasn't a really good way of porting ratings over (new people would still start with 1200, etc).

The bug I mentioned also seems to show someone's regular chess rating on the "open seeks" page for a 960 game, even if their 960 rating is different. I'm sure this has already been brought up - some bugs are expected with any new development, especially one as major as this.
By the way, Erik, since you posted in this thread: THANKS for the huge new feature! This is really exciting and I know it took a lot of work.

I agree that the ratings need to remain separate but would like to make this suggestion. When an established player with 100s of standard games plays their first 960 game it would seem fair for their initial 960 rating to be somehow correlated to their standard rating. Afterward complete isolation of ratings could be implemented. It is quite frustrating to see your rating plummet dramatically after being matched up against a 2200 rated standard player who happens to be playing his first 960 game against you in a tournament.
960 has its own rating. The points awarded are not influenced by an opponents online chess rating. It doesn't matter that someone is higher rated and therefore "better" in standard chess, because they might totally suck at 960.