InMotion went down internally when I added DC's IP to Router

I added our company's DNS from our domain controller to our router's DNS section. For some reason, that caused users' InMotion email in Outlook to stop working. It also caused the F2SI site to go down as well. I think this was only internally too because our boss was able to get to webmail and our website from the outside. Now I'm wondering, what do I have to do to get my DC's DNS onto the router without bringing down our InMotion site and email. Our domains are the same which I believe could be the issue. However, we cannot change our domain on the DC so what can we do to remedy this?