^ I had a post asking about waterproofing materials a few pages back, but no responses.
I've only waterproofed my AJKOs, but here's my take on it. Waterproof them once and leave it at that. I think problems arise after the first coat because the waterproofer itself is a liquid, so it beads up on top of the first coat and leads to an uneven appearance when it dries.
Like I said, my only experience is on Canvas shoes, but my method is to apply a single heavy coat over the shoe. Even on the first coat noticed the waterproofer beading on the nap of my AJKO's, so after a saturated the shoe I dabbed it lightly with a cloth to absorb any residual waterproofer and prevent spotting/beading.
Another thing I did was tape off the midsole and any area's I didn't need waterproofed. I've heard the silicone on the waterproofer can discolor plastic over time.