Hi nick1124:, I've merged your two threads on essentially the same topic, since you seem likely to reference them to each other, its best for everyone one to be on the same page.
To prevent soap formation in the production of biodiesel from methanol, its required to have everything scrupulously anhydrous. That is, start with everything anhydrous, keep everything anhydrous before you start, keep the reaction tightly sealed while it progresses, and then ... dry everything before you start. Then accept that there will still be some soap formed. Sorry to be flippant, but this is the gist of what I've read.
I'm describing bench-top glassware biodisel production. For industrial purposes, you want to apply industrial engineering concepts, that some people here can help you with. But again, its tricky.
For production in a shed on a farm, our citizen chemists can try to combine the above concepts as best they can.
The final answer needs some info from you regarding scale: are you paragraph one, two or three?