Spot,
As a beginner I found it nearly impossible to determine if my sanding was doing what I hoped when there were several different shades of filler and or bare metal showing. It's much more productive if you are sanding something that's a single color. As soon as I started covering the area with a coat or two of high-fill the low and high areas become so obvious even I could see them.
Don't be afraid to add filler over primer, it's perfectly okay. And don't be afraid to use that primer. You will sand most of it off with the 80 grit anyway... just think of it as a thick guide coat.
Another critical thing is DO NOT chase low spots with your sanding, fill them in. When you get to the 180 grit sanding step you should be able to effortlessly sand your 3M guide coat off completely without seeing any low or high spots. If you do, fill them with the 2-part glazing putty.
For the pros out there reading this keep in mind that I'm relaying my personal "body prep epiphany" experience so it may or may not be how you do it. All I know is that it works and it's simple enough for a novice to understand... and that addresses the OP's question.
