Given the wording of the spell, I have always treated it as the damage you heal (that is, the hits you roll) is the Damage Value in the Drain calculations.
There's no real specifics to say one way or the other is the RAW, but it seems like using "total damage on the character healed" would make Heal far less viable.
If you wanted to make it match first aid (pg. 252 of SR4A), it would be calculated based on how much you're "attempting to heal", which clearly suggests you could declare that you're trying to heal 5 of 9 wounds. Or, you could roll, the amount healed then sets the duration as the "attempting to heal" value, since you could be interrupted.