HH,
I assume you are in a boat if you are fishing deep water. One of the best methods for jigging, regardless of depth is to drag your jigs vs. "jigging" them. The boat should move very slow....1/10 to 2/10 mph. Let out enough line to allow the jig to drag the bottom and just let the jig sit on the bottom, the only thing moving the jig will be the movement of the boat. Kinda like a VERY slow troll but using a jig. If the bottom is snaggy, you will need to (1) decrease the speed of the boat and get the line more vertical or (2) use a heavier jig and get the line more vertical. Regardless of speed, depth, etc....use the lightest jig possible. Deepwater jigging in windy conditions is difficult, switch to a lindy rig to maintain bottom contact.
Other than jig weight, I dont do much different for deepwater jigging vs. shallow water jigging.