You put proofhide on both sides. Rub it in well, and leave it overnight.
Proofing the underside is optional, but useful to protect it fron water spray.

On the top, there is a danger of getting your clothes a bit contaminated, so you need to rub it in well before you ride.

I limitted myself to 5 mile rides for a few weeks (just going to work and back), until the saddle gained some shape.
Dont use too much proofhide, and dont use anything else. I found that one application was enough for the whole breakin period.