The power of the Dice compels you!
A standard NPC team size is equal to the number of players. How many teams you use is largely up to you, but start with equal numbers (or a squad of standard npc's plus a special lieutenant) and see how it rolls out, looking at per encounter rather than per adventure. SC characters bounce back fairly quickly.
Only roll to damage armour if it's being specifically targeted (or if the damage type specifically says to)
Hmm, you're right it doesn't make sense, I'd usually just ignore the damage striking the cover, if you want to start fiddling with it you could say amount the cover failed the save by is the damage value (to a maximum of the original damage)?