The cleanest way to accomplish this, if you have any cooperation from the DNS operator, is to use a subdomain for the AD and have the Unix server delegate that subdomain to the Windows DNS server. So if the Unix domain is domain.com, delegate internal.domain.com to Windows. Then everything's peachy.
Also, as OmegaXero describes, you may be able to set up some kind of primary/secondary system. I'd prefer the subdomain, though.
If you have to actually use the Unix server, then things get uglier. At the very least there are a bunch of DNS entries that must be entered on the Unix box in order for AD's LDAP/Kerberos stuff to work properly. Even once those are present, I'm guessing that there will be other issues that pop up to remind you that you're not following the true MS path, but I've never tried it myself. Or you could just allow dynamic updates, but there's no way for BIND to do that in a secure way that MS understands so then you're wide open.