Multisite + Buddypress community

OK, I have a project for a ministry I am helping out with. Previously, there was a main ministry site, a guys informational site and a girls informational. They were set up as static Web sites as subdomains of the main site. I am converting them to Wordpress sites. They want to add an online community for members to interact. They want it to be private. The girls and guys need to have access to separate gender separated forums/discussion board. We will also want to set up an online store in the future.

My first thought was that I could set up a multisite WP install with each site as a simple subdomain. http://www.domain.org/guys, http://www.domain.org/girls, http://www.domain.org/store etc.
I then installed Buddypress on the http://www.domain.org/forum site. I set up private groups in buddypress along with forums in each group. I have used WP several times previously and am still learning. I can feel my way through most of it. BP (and multisite) is completely brand new to me.

Some of the problems(at least as perceived by me) with the setup:
Each member of the guys or girls groups must be added by an administrator. That administrator must be "friends" with any member in order to add them to a private group.
Any members to any other site (store for example) must sign up through the buddypress registration. I know I need to learn more about how multisite and buddypress work together.

My questions for any willing advisors:
Is this the best way to accomplish what I need done? Would I be better off isolating the BP/forum in it's own separate install?
Are there any tips you can give me or point me in the right direction to learn more about such functionality in BP and Multisite?(I am good at teaching myself)
Any plugins that may be helpful?
Any other advice or suggestions? Let me know if I need to clarify any functionality or requirements.

Kris