I would make a separate save file and try a few different approaches.
Keep in mind, there are different ways to do everything in development and none are wrong, although some may be more efficient.
My Recommendations:
You will want to use containers for the sprites, I would then create a player family and use that for the logic, you wont need to re-write or copy any code or duplicate an event sheet, then use a family variable to declare which player is which when you get to that point, use that variable to assign to a player and instance of a player.
As for Family variables, they will assign each instance of that family member its own instance variable, they are not global so that won't be an issue, they simply automatically assign the variable which you can then access through the object itself.
I recommend opening up the RTS template to get a good look at containers and families.