I had similar problem when starting out. My root to success was this:
Use the debian perfect server guide
Then follow the name server guide
Use the ISPconfig3 DNS zone wizard to add DNS records
Add the sites in ISPConfig3
Allow 72 hours for all the DNS records to propogate
When checking to see if the new sites are working use the refresh page button or try from another computer if you're still getting the 'it works' page.
Patience was my biggest key to success.