Dont know if this will help...
I am also new to ISP Config 3.0. So I am not sure this will help.
We running MyDNS and are able to configure everything via ISP Config when you login as admin (or if your configured as a reseller/clinet). The DNS entries can be made in ISP Config 3... Just lookout for the DNS tab.
Just a tip... ISP Config has been upgraded to 126.96.36.199. I am finding it much more stable with the DNS that the previous one. Previously we had to restart MyDNS almost everytime when we added a new site. Now the server works like a bomb!