(Exerpts from a thread on Onelist FA-18 Forum/ML)
What you describe is indeed designating with the FLIR. If you have already designated with the radar, it is not strictly necessary to designate with the FLIR (FLIR in AUTOTRK mode) to keep the FLIR/LASER on target. Once the FLIR is slaved (GND STAB mode), it will continue to track the radar
designated target, and all TGT coupled systems will recognize this as the designated target.
Lets say you designate a target with the Radar, slave the FLIR, and decide you want to slew the FLIR to another target in GND STAB mode. Now, the FLIR/LASER will follow that second target, but all the aircraft's TGT coupled readouts (heading, distance, diamond marker in HUD) would STILL point to the first target, as that is the 'DESIGNATED GROUND TARGET' despite the fact that the FLIR is pointing at another target, and any Laser guided munition will guide toward the second target. This could screw you up if you used the heading info for the first target, and got out of parameters for the LGB guidance.
Clear as mud? Just remember this: For LGB delivery, the FLIR must point at the target, and you must drop the LGB 'in the basket'. For AUTO bombing, your target must be the DESIGNATED target, either by Radar, HUD Click or FLIR in AUTOTRK.
FLIR GND STAB: FLIR points at the designated target (designated by some other system)
FLIR AUTOTRK: FLIR is the target DESIGNATOR
What I originally thought, was that the FLIR in AUTOTRK mode would only track a piece of the ground/water and not a moving target, and that for a moving target to be tracked, the FLIR should be slaved to the radar in GMTT mode...turns out the FLIR WILL AutoTrack moving targets all by itself.