I've always used SUN ONE LDAP for the authentication in Cognos, it was simple and straight forward:
In Access Manager
Enter users domain/username token
Set their Userclass access to restrict what they could see.
That was all we had to do!
I have to set up the same but now pointing to MS Active directory.
What do I need to know/do, the documentation doesn't seem be very clear.
Many Thanks
Jason