I have two Google accounts as well:
- one Google Apps account (main, day-to-day email, first@lastname.org)
- one plain vanilla Gmail account (old, mostly unused)
When I learned that Google+ wouldn't work with Google Apps, I signed up using my old, vanilla Gmail account.
At this point, I really do feel like Google Apps account are second-class citizens in the Google world. I'm seriously considering switching back to my vanilla Gmail account for most things, and setting up email forwarding from my vanity email account.