There are a few things you need to consider:
VPN – are you setting up an internal VPN using MPLS or are you setting up a tunneling VPN through your DSL connection?
Domain – It is better if you setup a single domain once you’ve decided on your VPN. You should have at least 2 domain controllers. DB1 and APP1 should be the domain controllers for now, and WEB1 should be firewalled off and placed in a DMZ network. You don’t want web facing server part of your domain.
DNS – Your primary DNS server should be your local Domain controller APP1
Remote Desktop – On each server right click on My Computer. Click on properties. Click on the Remote tab and check Allow users to connect remotely to this computer. Once your VPN is up, you can connect to the servers using Remote Desktop.