I'm not too clear on the use of a target designator for something like a missile or mortar.

As I read it, it seems to say that if you're using a target designator, you have to make a ranged attack with the designator, using something like the Pistols skill.

My character uses a mortar mounted on a drone such that it fires and reloads automatically when I use the target designator. Basically, I highlight the target with the designator, signal the drone, it fires on the mark.

What skill would that work with?

Our GM has ruled that it's a Pistols skill roll with the designator.

If your designator is mounted on a weapon (I've got a character who slings one under a submachinegun), use the skill for the weapon it's mounted to.

If the designator is a separate, hand-held unit, I'm not sure there's specific rules for it, but I'd use the appropriate skill for a weapon of the same approximate size (if it's a rifle-sized designator for some reason, use Longarms).

Remote-designated mortars are rude, by the way... they're the same reason I've got a designator

I agree nothing like a man severent loaded mortar for support.

My old group had two designators one on our snipers gun the other on the gun-bunnies pistol as well as a few others though we normaly just slid them off the mounting if needed.