I light charcoal the old-fashioned way, in a pyramid shaped pile over the burner. The only time I use the chimney starter is when I'm cooking "hot and fast" on the SnS. In that case, I only light the gas for a couple of minutes. I do the same as MINIgrillin does, in that I'll put new charcoal on the bottom, and top it off with used.
After reading this thread, however, I may re-consider and start using the chimney more often.