Re: WPMU 2.6.1 and bbPress 1.0 Alpha
No, just install as normal in step 1 add the KEYS as they exist in your WPMU install and by the time you get to step 2 (integration) you should have a bb-config.php file. Add the SALTS in at the start of step 2 before you submit your integration details.
I made a change today to trunk… https://trac.bbpress.org/changeset/1747
This should allow you to successfully integrate and select an admin from the blog with ID of 1 (usually the primary blog) in your WPMU install as a keymaster.
Hopefully this will sort you out.