Appreciate the help.
I wanted it to be easy as possible for end-users. I ended up using intranet subdomains.
http://sales.domainname.tld goes to sales ibay
http://marketing.domainname.tld goes to marketing ibay
On a side note, if you put "sales." in virtual domains and map it to sales ibay, then
http://sales goes to the primary ibay. I couldn't redirect/rewrite this to sales ibay.
On another side note, you can add virtual servers to the smb.conf. This creates the illusion of multiple servers on the network. Of course
http://sales goes to the primary ibay. I couldn't redirect/rewrite this to sales ibay.