Just to clarify, you currently have an Apple ID that was created through iTunes or somewhere else, so it's using a third-party email address for the ID? If that's the case, then no, setting up an iCloud address for that (whether you get an @me.com or @icloud.com) does not automatically replace it, but you can use either to sign in to Apple services. I believe you do get the option of making it your primary, however, if you choose.
jW