Has anyone had any experience with using General Purpose Input Output pins on 3rd party boards?

The board will be proprietary but we are prototyping based on a few possible dev boards like Advantech boards
I found the GPIO pins to be something we would like to use since they are IDE'like ribbon cables that we can connect to a custom ISA socket.

Looking at the .NET Micro Framework but it uses drivers to interface with some popular boards.
Found the WDK as a possibility but other than creating a hello world driver I'm at a loss on how to connect to the cards pins.

Thanks for any help and sorry if this is not in the right forum.