The automatic PD functions work quite well in my experience. The rightmost box in the Combat Assignments window lets you set it up; missile fire controls let you set a number of missiles to launch per enemy missile, and you can set up one ship and use the Copy Assignments buttons to set it up for ships of the same class. I'm not sure about beams; I've only used my offensive particle beams in final defensive fire once, but that worked the same way, basically.
My escorts did a fine job of firing as soon as missile salvos appeared, and would also immediately launch on survivors (42% interception rate is a tricky number). I suspect that if you're getting extremely saturated, you might get slightly better results if you were to micromanage, but it worked well in more-or-less equal tonnage missile-only fights with Precursors.
Offensively, I think it's just a nightmare if you've got a lot of contacts. Generally if I intend to fire on more than one target I'll break up a task group (I typically do this with my fighter squadrons or gunboat flotillas) and then use the Copy assignments/targets. I imagine this wouldn't really help much once you're fighting more than small groups of Precursors, though.