I just did this with my wife and my new iPhones...
I just switched to iPhone from a Palm Pre, but my wife had been using an iPhone of one ilk or another for a few years (she switched from a 4 and got added back to our family plan). We both got new 4S's and I had to jump through some hoops to get this done. Our iTunes music and apps are under my account.
1. For my iPhone, I set it up as "new" and used my account during setup for iCloud, etc. All of the apps and music installed fine. iTunes, iCloud and Messages are all set to use my ID.
2. For her iPhone, I first tried restoring from an iCloud backup (she had been using my Apple ID on her 4), but that didn't work for us now that I was on an iPhone. The iCloud settings box won't let you override the account email/login. This was problematic as it caused both of our phones to sync my contact data and calendars, which isn't what we want. Also, Find Friends thought that she was me.
3. I started over and set hers up as a new iPhone. Because of this, we have to reinstall apps manually, add data, and rearrange things in the launcher. To get hers setup, here's what I had to do:
- Set her up with a new iCloud account during initial setup
- Go into Settings::Store::Apple ID and "Sign out" of her account and add mine.
- Make sure that Settings::Messages::Receive At::Apple ID was her ID. (I think it might have been setup fine, but just be sure, otherwise you end up sharing a single message queue.)
- Go to Settings::Siri::My Info and make sure that's set to be her ID.