That is the correct setup, especially for cooling purposes where you have the coolest card take the most heat. Both cards should actually clock to the slowest card, if not you can always balance them in mhz.
That's what I read elsewhere, but then I see articles like this one : forums.nvidia.com
that say you want the fastest GPU in the primary slot. (Search for "So be sure to have your fastest GPU in the primary slot"). Since the posts are from '09 I assume they are either wrong or something changed since then. Thoughts?