FYI, it doesn't seem that you can set up your app store account with a non-primary iCloud account. (I have a far, far older Apple account I use for music, books, and apps, and it existed long before .mac, .me, and iCloud). I'm funny about my purchases belonging to my own domain that I control the zone file for.
You can change music in the Music app, and it also changes TV.
I've *tried* changing the books app in the bookstore, but it won't let me. I think it isn't really trying to connect to my older account.
If anyone else has tips about how to split the functions for iCloud and purchases, let me know.