So my character normally has 3 boxes of physical stress capacity from his endurance, plus 4 more from supernatural toughness for a total of 7.  But if I get hit by magic I only have 3.  That's where we were getting confused.  So what happens if, for example, I get shot and take 3 boxes of physical stress, then get hit with a bolt of lightning for 3 more?  Am I taken out or not?  The 3 stress from the lightning would fill my 4th stress box (which isn't there when my catch is satisfied), but the physical damage I took first could fill the 4th box with no problems.
Here's your stress box: 000 (0000)
- You get shot for 5 stress by a gun:  00X (0000)  - armour absorbs 2, leaving you with 3 stress
- You get shot for 5 stress by a gun: 00X (X000) - armour absorbs 2, leaving you with 3 stress (which rolls over to your 4th box)
- You get shot for 2 stress by magic lightning: 0XX (X000) - armour is ignored for this attack, - you take a full 2 stress
- You get shot for 3 stress by magic Lighting:  XXX (X000) Minor consequence: 1st degree burn
So when you got shot on the last attack, for lighting, you are not allowed to use your toughness boxes or your armour.  You take 3 stress but your 3 box is full and you're not allowed to roll it over to your 4th because it's magic.  Instead, you soak up 2 of the 3 with a minor consequence.  This leaves you with 1 stress which fills your 1 box.
Make sense?
And does it matter which order I take the damage in?  If it was switched and I took the lightning bolt first and then got shot would it result in a different outcome?
If you switched the order of the damage, you would be in a better situation:
3 stress from magic = 00X (0000) then;
3 stress from gun  = 00X (X000).  Since your 3 box is already full, it can roll over to your 4th (but only because it's not magic)