Can I update both C & D drives?

You posted in Navigraph Hub category which is only for MSFS and MSFS Addons. I have moved it to the current category.

FMS Data Manager is used to update X-Plane 12.

Only one copy is supported.

For an unsupported work around, please see How to link two copies of XPlane12 to FMS Data Manager? - #2 by Ian

Cheers
Ian