I'm also not sure exactly how it works, but from the description it sounds like almost the exact opposite of what I'm wanting to do. xD
We don't want notifications to be sent to their personal for anything other than forgotten passwords because it forces them to use their school email. Sort of training the dog as it were.
Horrible analogy, but you get the point. But I love how close that was.
I however, love to do things the insane and stupid way. So I edited the source code.
First I added a custom profile field and made it required through the normal moodle interface.
Then I went into the Moodlelib.php library and edited all of the confirmation emails to go to to this alternate field's address instead. It looks like it worked, won't know for sure until it's in the wild though. xD Man I'm an idiot. I really ought to know better than to fool around with these systems.