Treat it like wax. Don't slop it on. Only so much will sink in at a time. Put on a thin coat, let it sink in, polish it off. Then ride it, do another thin coat, etc. The Brooks site has instructions similar to this.

The fenders on my TriCross are not that good, but they're enough to keep the bottom of the seat dry, so I didn't waste any on the bottom. (again, Brooks' recommendation)

Let us know if you notice any difference after a few Proofide applications.