Yes. This will make it harder to manage. Your purchases and app data are no longer included in a backup, since you use a separate account for both. Your messages, depending on how you configured it, will not back up. Music, I suppose you share an account, why you want this will sync with the owner's library, and you will only be able to play music when he / she is not.
Your personal Apple ID is designed for all this to sync so that you can expect to encounter problems.
Why do you want to use 3 separate Apple IDs?