IPhone – Do the two iPhones receive the messages

In iOS 6, your phone number and your Apple ID will be unified, so when you'll receive a iMessage or a Facetime call, they will appear on all your devices (iOS and Mac OS).

More info here.

So I think you just need to wait until this fall to resolve your problem !

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.)