Now that I have had some sleep I can think clearly.
I'd like to understand this DNS thing more.
All of our websites that we will be hosting, have outside DNS servers. Some of our sites are with GoDaddy, Register.com, and Network Solutions. I really do not want to change that as I fear putting all of my eggs in one basket. ie. a single web/mail/dns server. (Matter of fact, I'd rather split the mail part out and have that a seperate server also.) Anyways, they handle all of the A, cname, mx records and we just point them to our web/mail (ISPConfig) server.
My question is, when I create a site, should I not check the "create DNS" box and just never worry about the DNS settings on the ISPConfig box. Or, should I create a DNS record and in the nameserver fields put the outside nameservers that GoDaddy/Register.com supply us?