I am at a church, we have a 400A Main. We have 2 subpanels that are both 200A. We are building classrooms in another area and want to asdd a 100A subpanel. On the main panel there is about 12 empty spots where we can put breakers.

Can I put this subpanel in?

I do mostly VFDs and motors and looked through the code book and couldn't find a direct answer. Can you give me the code article also?

Yes you can put a sub-panel in, but you REALLY should have a qualified electrician come in and check things out for you.

I realize churches are almost always tight for money, and free/cheap help is good to have, but I see a LOT of hacky work from folks who have only a partial clue about electrical but a very generous heart. Sometimes this can be a dangerous combination.
PLEASE be sure to get whatever work is done verified by someone and definitely inspected. Churches and schools fall under some stringent codes and you do not want to make a mistake here.

Also, there is no one code that I can think of that expressly allows what you are doing. A load calc would be the only true deciding factor that I think would disallow it.