The profiles command in Yosemite (and Mavericks for that matter), can configure profiles to install at the next boot, rather than immediately. Use the -s to define a startup profile and take note that if it fails, the profile will attempt to install at each subsequent reboot until installed. To use the command, simply add a -s then the -F for the profile and the -f to automatically confirm, as follows (and I like to throw in a -v usually for good measure):
profiles -s -F /Profiles/SuperAwesome.mobileconfig -f -v
And that’s it. Nice and easy and you now have profiles that only activate when a computer is started up.