You calculate hits first, then roll stealth, for example:
You get hit by 4 phaser-1s in kill zone, 3 impact on the shields, one bypasses shields, this generates 6 hits on the shields (from killzone) and 2 rolls on the damage table. Before these are rolled, you roll for stealth. Say you get a 1,2,3,4,5 and a 6 against the hits on the shields, this stops 2 so you take 4 shield damage. Then you roll two dice against the hits through the shield, say you roll a 3 and a 5, this stops one of them, so your opponent then rolls once on the damage table.
Then your opponent fires at you with one type R plasma torpedo, you hit it three times with defensive fire reducing it to 4 dice (note the torpedo is not harder to hit from you being in a dust cloud, stealth only applies to ships, not seeking weapons). Your opponent then rolls 4 dice to determine the number of hits, lets say she scores 14 hits, then you roll 14 dice for your stealth. You then apply the remaining damage to your shields first, then your hull if you run out of shields.
Then you point out that since I clearly choose a war eagle for the example ship (what else has 4 phaser-1s and a type R torpedo) your opponent is cheating since under-powered means she can't fire both the phasers and the type R on the same turn with that ship.