So I went on somewhat of a wet, muddy ride on Saturday, so I decided to spray the mud off the bike with the garden hose, let it dry, and then run my chain through my pot of wax again. This time I tried the OP's drape method, leaving the chain on the bike. I couldn't really get it to drape very well through my pot for some reason. I had it on the smallest chain ring and next to smallest cog, and was trying to turn the cassette backwards so the chain would go through the wax as I held the RD cage forward. I guess the angles of everything just didn't want to work very well.

Perhaps that's why the OP said he removes the chain from the rings and lets it drape over the BB. That probably works better. I might stick a piece of electrical tape over the BB at the point of chain contact and give it a try that way.