If I understand you correctly you want to change your iTunes Apple ID to your me.com Apple ID and it says you are trying to change your iTunes Apple ID to and Apple ID already in use. That makes sense. Also, you can not merge 2 Apple ID's into one. I think you are kind of stuck with what you are trying to do.
For me, my wife and I like to share our iTunes Account but nothing else so this is not a problem for me. We each have a MobileMe Account for all of our personal stuff (mail, calendar, contacts, etc) and we share the iTunes Account for Purchased items like Apps, Music and Movies.
However, at this point we are not allowed to upgrade our MobileMe accounts to iCloud because it is in Beta. Following link will be used once iCloud is out of Beta.
http://www.me.com/upgrade