As BIND gets installed as DNS server with the perfect debian setup guide for ispconfig, should i use my own server as the first nameserver for domains that i am hosting on my server then?
You can do it however you like. If another name server handles your DNS records, then don't change anything. If you want to use your own name server though, then you have to create all necessary records using ISPConfig's DNS-Manager and tell the registrar where you registered the domains that your ISPConfig server is the new primary DNS for these domains. The DNS-Manager is just an option for those who want to run their own name servers.
