PXI Embedded Controllers are computers, so it is possible to do many things you would with a desktop PC. You could set up the second harddrive as a slave, however, you would need to provide the cabling to attach a second harddrive. Due to the compact build of the PXI embedded controllers, it could be difficult to connect both harddrives at the same time. It may require "taking apart" the controller to achieve this.
An alternative would be to configure the ghosting program to work over a network. Then you could ghost the 2nd harddrive without any modification to the PXI controller.