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The best way to keep all of your information separate is for your wife to have her own User Account on the computer and her own Apple ID for her iPhone.
That way, all of her email, contacts, calendars, music, etc. will be separate from yours.
The articles below will review how the Apple ID and iCloud works.
You can click on the links to see more details and screen shots.
An Apple ID is a user name you use for everything you do with Apple. Creating an account for an Apple service, such as the iTunes Store or the App Store, creates an Apple ID. Apple ID allows you to access other Apple services. You don't have to create a new account for each service—just use your Apple ID.
You may already have an Apple ID, and you only need one for everything you do with Apple. If you aren't sure, visit My Apple ID and click Find your Apple ID.
If you don't have an Apple ID, you can create one at My Apple ID. You can also create one by signing up for an Apple service (such as an iTunes Store or iCloud). You should use your primary email address as your Apple ID.
What is iCloud?
iCloud stores your music, photos, apps, contacts, calendars, and more, and wirelessly pushes them to your iOS devices and your computers. iCloud is integrated with your apps, so everything happens automatically.
For example, if you buy a song in iTunes on a Mac or Windows computer, it appears on your iPod touch and iPad. When you snap a photo on your iPhone it’s automatically sent to your iPad. You can start creating a Pages document on your iPhone, and put the finishing touches on it from your iPad. There’s no need to dock your iOS device or sync it to your computer.
Setup iCloud on iPad, iPhone, Mac and Windows PC
I hope this information helps ....
Have a great day!
Settings>iCloud>Delete account. Then add a new one with her Apple ID.
Settings>Messages>Apple ID>Sign out. Then sign in with her Apple ID.
Settings>FaceTime>Apple ID>Sign out. Then Sign in with her Apple ID.
Settings>iTunes and App Stores. Keep your ID in all devices to purchase ones for each app or music.