Hi my partner used my email address and iTunes account to set up his iPhone and now both our phones have merged! Does anyone know how to separate these? Can he still use our iTunes account with a different Id or email! Please help!!

You need seperate Apple IDs for iCloud. iTunes and iCloud are not the same.

Create a new Apple ID > https://appleid.apple.com/cgi-bin/WebObjects/MyAppleId.woa/

On one of the devices go Settings > iCloud > Delete Account > Sign in with the new Apple ID

This will seperate your Contacts and Messages. You both can continue to use the same Apple ID for iTunes and share apps and music

Several things here so let me attempt to clarify.

For iCloud the reason the contacts where removed from he other device is because you updated your contacts, in this case deleted them, and then iCloud updated the other device to match. By deleting the iCloud account on the device it will stop the device from using that iCloud account and therefore nothing will change on the other device. By using a seperate Apple ID you can still use the features of iCloud, Find My iPhone comes to mind, without your content (contacts, message etc.) merging with the other device

For iTunes, you cannot use two Apple IDs for one account however if you use the same account iTunes on your computer will keep the content on each device seperate very nicely. You can also configure the settings for iTunes and the App store on each device to keep the content from automatically downloading to the other device. What I meant by share apps and music is this. What happens if you find a game, lets say Minecraft, that you really like and it cost, as Mincraft cost, $6.99USD. You buy it and play for a while and then you realize that your husband really likes the game as well. If you both use the same Apple ID for iTunes he can download the $7.00ish game to his device at no additional charge. If you use seperate Apple IDs for iTunes well... it look like he will also be paying for the game to have it on his account. Same goes for Music and Movies

I hope that clears things up. Let me know if you have anymore question.

I don't think you can have two ID's on one ITune account. When you look at "managing accounts," I don't see where youk can add another account. You're just going to have to share the info with your hubby!