What fahadsadah said - you contorl this via MX records -but I believe you meant you want the MX for one FQDN to be handled by google, and the other (mailmain.domain.com) to be handled by a services somewhere else - same thing - just separate MX records in DNS (and don't forget the SPF and other records that go along with it to make life easy)
Yes. You can just set up MX records separately for the two, enrolling them both in Google Apps separately.
What fahadsadah said - you contorl this via MX records -but I believe you meant you want the MX for one FQDN to be handled by google, and the other (mailmain.domain.com) to be handled by a services somewhere else - same thing - just separate MX records in DNS (and don't forget the SPF and other records that go along with it to make life easy)