IPhone – Can iMessages be deleted permanently or at least kept either on a phone or a computer, but not both

Based off of my tests, when you choose what email addresses you want to use to receive iMessages, this is set on a per device basis. It's true that each Apple ID will have the same verified email addresses wherever you look. But the checklist in each devices' iMessage settings allows you to choose which email addresses you want to receive messages on that device.

So if you added the one from your iPod Touch as an address to receive at on your iPhone, only one thing would change: you would begin receiving messages sent to that email address on your iPhone.

All this being said, I would recommend you use only one Apple ID for all of your iMessage needs. Changing it around at first will seem a little tricky but should pay off in the end. (Tap the 'Apple ID: ______' button in your iMessage settings and you can change it out without messing up anything else Apple ID-related on your device.)

As you can see in the first screenshot, you can set a number of email addresses by which you can receive messages at on your phone. However, as the second screenshot shows, you can only have one Apple ID connected to a device at a time.

You might be thinking, "Ok, can't I just add her Apple ID email address to my phone?"

The answer is no. Any time you add an email address to your iMessage account, the email is verified with Apple. If you attempt to add an email address associated with another Apple ID, Apple will decline it and neither iPhone nor OS X will not allow you to add the email address.

Conclusion: Unfortunately, there is no way to do this with iPhone or OS X. You could do what was previously suggested and set up a secondary account on your Mac (if you have one) and link that account to her Apple ID and use Message there to view the exchanges, but to specifically answer your question, OS X does not accept more than one Apple ID for iMessage per user and iPhone does not accept more than one Apple ID for iMessage either.