I was writing up a couple ways to do this, and it seems, to me, to complicate things.
One factor I found while thinking of this is if you are going to try and use the DNN registration for 1 of them, or have 2 custom registration pages.
Why do you need two? Could you create some options on the custom page to make it behave the way you need for the other one?
Depending on why you need two, and public links to them both, I'd wager it is complicating things, and 1 registration form can probably be sufficent, but I don't know your exact situation, so I can't say for sure.
I've had to have 3 different 'groups' register on a site of mine, and I was able to do it by ading a few check boxes and radion buttons,
So any extra info on why you want/need 2 should help understand how to best accomplish the goal.