I need some help here. Once I registered my own DNS with godaddy (i.e. ns1.mysite.com, ns2.mysite.com), can I use these with other registrars?

Meaning, some of my domains are at register.com, can I just change the NS info over at register.com for those to mysite.com? Or do I have to register my NS with register.com as well?

Thanks a bundle!

yes. Godaddy is just an agent. The registry is open to the world at large.

I would be very surprised if you could make changes to the domains registered at Godaddy from your other account at register.com. The standard procedure is to login to your account at the registrar where you registered the domains, in this case godaddy.com. I don't think that both registrars share the same database and one can control the domains registered at the other.

Of course, you can always try and see if what you want is possible. Let us know if you are successful.