I was thinking of painting my stormtoopers with some shoulder markings to identify them, would look more natural then a sticker placed on the base.

Coloured right shoulder pads, plus one to three 'rank flashes' of white will make it easy to track. Although quite often I just put damage tokens on the trooper's base, to be honest.

(Non elite) Troopers do drop like flies. A trooper in line of sight of jyn will probably die before he gets to move as often as not if she has strain to trigger her ability.

But yes, most of the time stormtroopers should be acting as guards or speedbumps rather than advancing out to attack. The rebels have to come to you, after all.