Since I had several supernatural players with no magic (but lots of toughness/recovery powers), I did it that if the consequence gets tagged, you get a FP regardless of if you healed it or not. Any others that remained that were untagged also got a FP. So...
Ghoul takes a mild, heals it, takes a mild, it is tagged (1FP), heals it, takes another mild and a moderate (2FP) cashes out, he'd get 3 fate points.
At the table, I'd also keep a constantly moving pile of FP for each player. If they received a consequence, the pile would grow. If they healed it before it was tagged, it was taken away. It was easier for me to manage that way.