Not sure how much an affidavit will help in that the prosecution cannot cross examine an affidavit.
I will slightly disagree with antrc's post. Who the car belonged to is not so much an issue... MJ was found behind the back seat and either one (Bill or Jon) could have tossed it back there. "Possession in law" is not about ownership or physical possession. it is more about "access/dominion and control" and it seems that in this case, both Bill and Jon were in possession. Which is the likely reason why the citation was issued in spite of Bill's admission.
I'm sure the citation is charging your son with a specific statute. Posting that code section number may aid in determining how you should proceed.
Legal definition of "possession"

