While I have agreed in the past that negatives seem intuitively to be BAD and positives GOOD, in practice in several games what tends to happen is the mental calculation first, then the rolling. That means (for my circle of friends anyway) we tend to modify the target number, then roll, and look for dice showing that number or higher - even when the game system demands a roll followed by modifiers, like Defiance.
The range brackets (common to LOS, PS, and the aforementioned Defiance) encourage this. You start the sequence by asking "what is my target number at this range?" I think that's the key to it. As long as you're looking up your kill number, it seems the appropriate time to modify it. Otherwise you end up saying "What is my kill number at that range? Oh it's a four" *rolls dice* "Hey, I got a four. But, oh wait, that's not really the number I need, because +1 for stationary, -2 for the nachtmacher, etc, that dice is really only a 3."
Now, I THINK that this makes most sense with multiple dice. When you're only rolling one it's very simple to say "It's a four, plus one, minus two, aw! Only a three." But if you're rolling three or four dice at once it tends to create a bit of overload: "It's a four plus one minus two, and a one plus one minus two, and a five plus one minus two, and a six plus one minus two, so that makes it 3, 0, 4 and 5."
Anybody got any thoughts on this or am I over-analysing?