Smear it on either way. I run a bead of it between the welt and uppers. Get out the hair dryer and melt it. The leather will suck it up. Let them sit for a day and then wipe them down with a rag and you're done. I do this on a regular basis and my boots are pretty much waterproof. I've stood in ankle deep water and mud all day without getting wet feet.
Hair dryer is a good trick. Thanks.