TrainingWheels,
The way I understand it (disclaimer, I operate an aircraft with an FMS, however other FMS's could be different), is that the FMS updates its position mainly using the inbuilt GPS, and then uses VOR and DME in the event that the GPS stops working. However, there is also a way to tell the FMS which one you want it to update exclusively by (ie. if for some reason you want it to stop using the GPS, then just select VOR and DME).
I think I just confused myself writing that, so might be back to the book to update myself on exactly how it works, but that's basically the gist of it.
morno