OP, please excuse the hijack.
I believe you and I are dealing with variations of the same problem.
We do use Find My iPhone, which is enabled under iCloud Settings with the primary Apple ID and needs to remain the same (along with the App Store, as well, for app sharing.) We are geographically located 800 miles apart.
My research seems to indicate that an additional Apple ID can be set up on his iPhone under
Settings > Mail, Contacts & Calendar > Accounts > Add Account > iCloud > Scroll to bottom of page and choose Get a Free Apple ID. This won't remove the primary ID but should then be set up using his own Gmail address (on record from a previous attempt turning ON iMessage, which then replaced my phone number with his for everything. Signing in to my Apple account online allowed me to correct this after he turned iMessage OFF.) We are seeking to avoid this scramble yet be able to use iMessage on both iPhones. FaceTime works via phone numbers.
Our situation is reversed in that I'm the original Apple ID user (2009) and whenever I upgrade my iPhone I pass the previous one along to my son. He's presently using my previous iPhone 4 while I use iP5 (having chosen to wait until 2014, 3rd Quarter, to upgrade my iPhone and pass iP5 along.) He bought a MacBook Air yesterday for work and as soon as he set it up, I got the popup Apple message telling me that his new Mac was signed into iMessage & FaceTime with the original Apple ID and both of our email addresses. He sees no way to uncheck my primary email address but that may be because it's tied to the only existing Apple ID. Creating a secondary ID for him might remedy that situation.
At the moment, iMessage is turned OFF for him on his iPhone in order to keep from getting iMessages meant for me.
This stuff gives me a headache. It would be easier to just use 2 separate Apple IDs for everything but it would not be better for our purposes, which are:
SHARE: Find My iPhone, App Store (original Apple ID)
SEPARATE: iMessage, FaceTime (secondary ID, via iCloud)