There should be no problem at all. You simply cant use Google+ with either of them, since Google Profiles are not available with Google Apps account. At least with those domains, which are migrated to the "new" infrastructure.

Google stated multiple times that Profile service should be available to Apps users in "few weeks", but they never kept that promise.

My main identity also is on Google Apps, so Google+ is not relevant at all. Even though that dissapoints me, I'm not going to bash my head against the wall.