Are you trying to connect two subnets together via VPN and then have all the clients go through one WinGate for internet connectivity? If so this is certainly possible and WGIC will work as expected in this setup. ie Subnet 1 is running a full copy of WinGate with VPN, and subnet 2 is running just a VPN version of WinGate. A client on subnet 2, should have the rip client running on it (available from
http://www.wingate.com/download.php ) so that it knows of subnet 1. Then install the WGIC on this subnet 2 client, and point it to the WinGate server on subnet 1. This is a tested and proved scenario.
As for the first part of your question, thats tricky. If you want to allow you clients NAT access for some apps, as well as using WGIC for specific apps, the easiest way to set it up is to manually enter the apps in to the WGIC on the client and specify either 'local' (WGIC not used for these) or Mixed / Global (the WGIC will be used). If you don't want to do this, then you're going to have to get detailed with your policies on the WinGate server, creating a mixture of policies to only allow certain apps to use the WRP service, while in the ENS properties blocking ports of apps that you dont want to give any access to.
For some more information about WRP look at the overview / comparisons doc found at:
http://www.wingate.com/resources.php
Regards
Neil