Ok, this is what I've been able to come up with.
The sensor on the Thermostat housing goes to the Dashboard gauge. The other sensor that sits at a 45 degree angle and screws into the manifold is also a temp sender, but that goes directly to the computer.
So, I would think that if you take out the Sender from the Thermostat housing, and put the aftermarket sender in its place, it will work just fine. Just remember to ground the OEM sender wire, otherwise you will get a "Check Gauges" light... I would presume... I will update when I get my water and tranny temp gauges. I might even take a few pics.