The best foundation for a new paint job is the factory one as long as it is not compromised, crazed / cracked / peeling.
Once you expose bare steel you need to prime it with a rust inhibitive self etching primer, then an epoxy primer, and / or a high build urethane primer.
I never apply filler over anything except bare clean 24 grit ground steel. I have used Dupont 244S on steel then applied filler. 244S is a metal etcher.
As far as your fenders peeling, I would guess that they are aftermarket and were not sanded before he painted them. I see this allot from armatures. they think the shinny black primer that comes on aftermarket parts is ready for paint. At the least it needs to be sanded. You always alway sand a dry or cured product that has been applied to a panel to achieve mechanical bond. Some primers and sealers are meant to sprayed wet over wet. In other words you spray it then within the window directed on the can you can apply another coat of the second product over it without sanding.
If you have a Borders store near you, go see if they have or can order you a couple books on body work. Hot rod and four wheel magazines have articles allot too, but I have seen them do stuff that is not common practice. That being said there is more than one right way to do body work!
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