How do I allocate variable damage to multi-wound models?
With variable damage against multi-wound models (or models with a Feel No Pain equiv.) you need to roll the damage rolls one at a time. The damage is not rolled and then assigned. The only choice you would have is if you had a weapon whose profile changed based on hit/wound roll (for example d6 instead of d3 on a 6 to wound). In this case you would make two groups of wound pools, and the firing player could decide which should be applied first, the defending player would then make the saves against these. If the defending models had differing saves (or some had FNP) the saves and damage rolls would need to be made individually.

The important thing to remember is that technically group rolling is a shortcut. Each weapon is intended to be fired individually. This is of course tedious, so where possible, when it doesn't actually matter, we group rolls together.