I have my KWS set up on trigger 2 in a second fire group, along with my lasers on trigger one. I can start to strip off the shields while scanning. When the scan is complete, I just switch over to fire group 1 which changes out the KWS to multi cannons. Seems to work for me. Your mileage may vary. Have fun out there.
Have the same setup, only with cannons in place of multi. But I also utilize my Voice Attack, so my first action is to go into scan mode, which targets the ship, switches to the first fire group, and holds down the secondary fire for me. All I have to do is keep them in the target area until complete, working the shields and hull down with my lasers. Once complete, I switch over to combat mode, bringing out the cannons, and finish the job.
