HardCMP will show you more clearly the placement and direction of the hardpoints, so you can move them more precisely into the position you want.
Version 23 has direction boxes and arrows to help you better, but it doesn’t work on my old laptop, so I use v18 which doesn’t show the direction arrows.
You can have several shield mounts, I have used up to 5 on my big ships, placing them 150 metres apart to cover the length/width of the ship. I used 150 metre shield bubbles. You can also design larger shield bubbles for them instead and maybe use 2-3.
I don’t know if there would be any problems using more shields on a large ship, or the max number, but I didn’t have any troubles with them.
I can’t help you with the damage stubs, I never used them.
But someone else will be able to help with that.