Eh, if it's not actively being used, it's not going to be drawing much power or making much extra heat. Hell, even if it was being used, it still wouldn't on both fronts. The power control of these new processors is prettty damn impressive.
It basically depends on the setting in BIOS/EFI. Most boards are configured to disable the CPU-GPU if a discrete adapter is present. It doesn't hurt to check that setting.
I never knew you could disable it. I figured it was disabled by default if yoru not using the Onboard video card. If your using Lucid Logix I would assume its being used to some extent with Discreet videocards.