Apple doesn't care what you buy with your account. When I got my iPad, I used an old account I had from 2006 when I first got an iPod. As far as Apple is concerned, one account is all they need.
While your best bet was to have just used the old account from the beginning, you can put stuff on the iPad using either the old account or the new account. The only hassle is, when doing updates or messing about with iTunes, you'll have to log in/out to work with/switch between the accounts.
I would recommend you use the account with the most purchases recorded against it. That way, your odds are better that the updates will be more on that one (more items). Just use one from now on and you'll lessen your hassle. And, if you can, as DefBref said, if you haven't used the new one to buy apps, just don't use it.
Marilyn