Managing multiple RTC projects

I've looked through some of the online help and also searched through
messages here to try to get a sense of how to use projects to manage
various development efforts, but it's still not very clear to me.

We will initially be piloting with one med/large group (~80 users), and
one small group (starting with ~5 users). The two development efforts
are completely independent from each other. I don't believe there's any
issue with visibility of each other's artifacts by the other team, but
we want to make sure things such as querying, reporting, etc. are scoped
on the project level and not across projects.

Are there documented best practices yet, or perhaps this is covered
somewhere I haven't located yet, on use of separate repositories versus
projects for managing various development efforts?

We have the potential need to support 100's of projects, and I frankly
can't envision using a separate repository for each of these. So, I'm
trying to understand when to use projects versus repositories to manage
these efforts.

Thanks, Brian