To begin with, I would like to try to explain Apple's confusing nomenclature in regard to iCloud.
Apple have called the whole cloud thing iCloud, there are a number of features under the iCloud umbrella, some of which require their own login. iTunes is one of these, another is what Apple have unfortunately also called iCloud too.
You can use the same Apple ID (account) to login to both iCloud and iTunes, but you don't need to and often users will login to each service using a different ID.
The part that you need to remember is that the services available when you log into iCloud are completely different and unrelated to those when you log in to iTunes. Your iCloud login enables mail, contacts, calendars, find my phone, Back to My Mac, Documents & Data sharing and photostream, it does not affect any of your iTunes services.