Prep work is the biggest deal. What I learned in collision class when I was in high school is do bondo before you lay any primer. So if it were me I would take it to bare metal and bondo it, etc but then again you will have the problem of rust the next mourning. I was just taught to grind away all paint and everything before laying bondo down. I am sure it's ok to lay on top of the primer, etc but I only did it that way one time and the car I am doing it on is not primered yet I still have the front clip to fill with this 3M Automix 5895 Plastic Repair stuff.
Good luck and pictures would be great, I wanna see how it comes out too.