Is there a way to change the names of the college teams for rookies that are generated for the draft?

You can edit the players by clicking the commissioner icon in the lower left corner and choosing the edit player option from that screen. Then when you are done click the other gray icon to go back to your player

I appreciate the response, I was hoping that it would just pull from a new list of colleges that I set up. I guess I could run a DDS College league along with the pro league.

Oh if you want to do that you could always edit the default database with something like SQLite Studio and change them to what you want but it will affect all leagues you are using