To answer the original poster's question, you will still be able to keep your eNom account... but if you try and contact eNom directly they might tell you to contact ModernBill first. They will ALWAYS be your "parent" account, so it does not matter if you continue to use modernbill (the software) or not... since your eNom account will always remain under them and they are supposed to be your "first line" for support of your enom account.
With regard to the AWBS software and it's retarded template system.. you should take a look at the "bare" theme. It is designed to just use a simple header/footer and does not try to take over your entire website. This way, it works just like all the rest of the billing systems and you don't have to use the stupid (and ugly) "whole website" templates from awbs.