Yeah two variable sounds good because you would use one for the normal damage, and if bullet collides with that target then apply damage from the second variable.
Have you tried using global variables? You can have one for equipped weapon, damage, rate of fire etc. Then in events you change the variable values based on equipped weapon rather than use instance variables on the objects.
Not sure what you mean about splitting enemies, can't see how the game works so it's difficult. In general though you should be able to do what you want with events.