how to set up a non-wp database as well

Hello out there ..

I am more or less a newbie with wordpress but I am thinking about moving a rather large site to wordpress. I learned that I can develop my own theme thus can at least try to keep my structure. But can I also keep my databases running? And if so, how do I do this? There is php but so far I only found how to work on wp-db.
Maybe there is a simple answer or a question about this exists already, but I just did not find it (sorry if so)
Any help is highly appreciated.