Unfortunately, you can't change the location where Notification Center Alerts and Banners appear. This is a huge gripe of mine as well, and I highly encourage you to complain about this issue to Apple here:
Hopefully they will one day change this. I also have not been able to find or formulate any hacks.
I, too, am annoyed by it covering up controls in my modeling applications, tabs in my browser, etc.
You can move the Notification Center to another screen, however your entire menu bar goes with it. When you have more than one monitor active, open up System Preferences > Displays > Arrangement. Click and drag the white bar inside one of the squares representing your current primary monitor and drag it to another monitor.
Good luck, and keep spreading the word that we need to tell Apple to make this experience better.