Help fill holes in Trunk lid

So in my 66 dart, it had the wrong trunk trim, which was too heavy and caused trunk to not fully open. I finally found the original Trim and installed it (the original holes were still there.) But now I have 6 big (1.4in) holes to fill and paint. What is my best bet for this fix? I have never done any body work. Also I notice there is a fair amount of bondo filler at the top of the trunk lid. I plan on removing the lid and repainting the entire thing BLACK.
I guess the prev owner didnt remove the trim when he repainted the car. thus the red. and yes the light bodies are painted black. trunk lid - 1.jpg