Hi Brian. Yes, in order to separate your apps and messages from hers, you will want to set up a new Apple ID and enter the account in a few places.
First, go to Settings -> iCloud, scroll to the bottom of the screen and tap "Sign Out", then sign back in with your own ID
Next go to Settings -> iTunes & App Store, and select the ID at the top of the screen and tap "Sign Out", then sign in with your new ID.
Once that is done, go to Settings -> Messages, and go to "Send & Receive". Remove any addresses belonging to the old account, and add your new Apple ID so messages sent to your account can be received
Please let me know if you have any questions and I will be happy to assist further. Thanks again!