I'm lost too

do you mean to say that you keep Win 2003 server because Zentyal doesn't work as expected ?
If yes, then let me explain something:
- if, for your network zone, you maintain entries in Windows server DNS
and if you define Zentyal as DNS server for this same zone without maintaining entries in Zentyal, then do not be surprised that it doesn't work 5meaning Zentyal will not resolve names for this zone he is suppose to maintain).
- if you want Zentyal to also resolve names for DHCP clients, Zentyal
has to be DHCP server.
- except for DHCP client, Zentyal, as DNS, will never "recognize" intranet computers. You do have to maintain it manually.
Once all of this is done, then, trust me, Zentyal can act as efficient DHCP and DNS server. And if used with transparent proxy, then half_life's point is meaningful: activate forwarding feature at Zentyal DNS level