Would it be enough to do only the dnsmasq part on the ispconfig 3 server? from the article at http://www.howtoforge.com/mydns_mydnsconfig_dnsmasp_on_ubuntu_edgy:
MyDNS does not contain a DNS resolver that is able to resolve DNS records that MyDNS is not athoritive for. In the next step I will install and configure the DNS resolver and cache DNSMasq to act as a local DNS resolver and configure MyDNS to use DNSMasq to resolve external domains. If you don't want your server to resolve external domains, you can skip this part.
Create a DNS Resolver on IP 127.0.0.1:
apt-get install dnsmasq
This installs the dnsmasq Ubuntu package. Now we will have to edit the DNSMasq and MyDNS configuration files to ensure that both pacakges won't listen on the same port on all IP addresses.
bind-interfacesNow edit the mydns.conf file to configure MyDNS to not listen on 127.0.0.1:
no-listen = 127.0.0.1
recursive = 127.0.0.1Then edit /etc/resolv.conf:
and add the following line as first line so that the DNSMasq DNS-Cache is used for all local DNS queries, too: