this all depends on what you want each of them to manage. If you want some hosts within yourdomain.com to be handled in AD, and some to be handled in BIND (assuming that's the DNS program you're using), then you will have some major issues. If you want one to replicate the other, that's doable. The way lots of companies get the two to play together nicely is to assign a subdomain to AD and let it be authoritative. So, you'd have BIND running on linux, responsible for *.yourdomain.com. AD running on windows would be responsible for *.corp.yourdomain.com (or whatever you want to call it - lots of people do one per windows domain and lots of people use CORP ;-)).
DNS architecture at an enterprise level is actually a somewhat complex thing. It's a good idea to work it all out on paper (or whiteboard) before you try to implement anything. find yourself a systems architect and build something cool