Selby, what you have said is contradictory:
If, as you suspect, air forced into the vent is exiting through the head, then the stinky air must be passing through a duckbill valve that is not acting as a one way valve, ie: the joker valve is not working correctly.
If you replaced the joker valve, and you are confident that it is functioning correctly, than the odor is not coming from air forced into the holding tank vent.
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If you simply want water in the bottom, then the correct way to do it is with the vented loop, for which I do not have instructions or diagrams. Perhaps the forum moderator, Vic Willman, will be able to help you with that when he gets back from vacation.
But if you are attempting to diagnose an odor issue, it is unlikely that there will be any difference between a bowl with no water and a bowl with water. If the joker valve is functioning correctly, the odor issue lies elsewhere.