I upgraded my phone to an Iphone and got my son one as well. I set up both with my Apple Id. How can I go back and change his so he doesn't keep deleting my contacts?

To migrate his phone to a new account, start by saving any photo stream photos that he wants to keep to his camera roll (unless already there) by opening your my photo stream album, tapping Select, tapping the photos, tap the share icon (box with upward facing arrow), then tapping Save to Camera Roll. If he is syncing notes with iCloud that he wants to keep, you'll need to open each of them and email them to him so you can later copy and paste the text into new notes created in his new account. Then go to Settings>iCloud, tap Delete Account (which only deletes it from this iPhone, not from iCloud; your phone won't be effected by this), provide the password to turn off Find My iPhone and choose Keep on My iPhone when prompted. Then sign back in with a different Apple ID to create his new account and choose Merge to upload the data.

Once you are on separate accounts, you can each go to icloud.com and delete each other's data from your accounts.