I'm not 100% certain as I haven't seen it coded, but...
I would suspect that bubbles are applied like shield blocks, to the damage making it to you. In other words, if you avoid getting hit the bubble will not soak anything from that attack, or force you to not avoid the hit and soak some of the damage. Also, it will soak damage that gets to you after the relevant reductions (armor, stance, etc).
So, if the boss is hitting you for 50k unmitigated damage, and after your survival bits and pieces you're only taking 10k hits. The bubble will not soak from the 50k, but from the 10k.
I'm not entirely sure. I expect the other possibility is that it is soaking from the 50k and so your damage reductions are applying to the leftover. Either way the end result should be roughly the same, but in the latter case your armor and reductions will be a little less effective.
50k reduced through armor (say 65%) and stance (say 10%) will be 15.75k (68.5% reduction or 34.25k reduced), bubble for 2k will knock that down to 13.75k.
50k reduced by a 2k bubble will be 48k, then through armor and stance will be 15.12k (32.88k reduced, 65.76% of the original total).
I expect it's the former.