The key to getting the maximum screen-shaking and intimidation effect is to group two AC2's in each arm, chain fire, and then when you've got an alternating firing-pattern between the two, hold your finger on your Alpha-Strike button. If you get it right, you'll start unloading ammunition into your target an obscene rate of fire. Most Atlas pilots even flee when the barrage starts. (I should also note that you need to have endo-steel and ferro fibrous in order to cram in the most amount of ammunition, and that you have to deal with being a little bit slow with the 4X's default engine) Take an XL-engine with a Jagermech, and this problem is remedied, however you'll have to be more careful.
I tend to leave the ammo in the legs, in the head, and in the CT (unless it's AMS or MG ammo). Most people are more interested in shooting your giant torsos, so keeping them away from there is the better option. They could try to shoot your legs, but if they fail to do that in short order - You'll tear them apart. I figured that if they manage to strip enough armor to blow up the ammo in my CT, I'm probably dead anyways, so I don't mind not running around with CASE.