Brooks recommends applying a layer of proofide to the bottom of the saddle. However, you should _not_ wipe this layer off after it sets. Just leave it on, and it will protect the underside.
Personally, I also recommend fenders for a bike that you plan to use frequently in the rain. This will also drastically reduce the amount of water that splashes up into the underside of your saddle. However, only a "permanent" full-size fender will really provide this protection — removable ones don't protect the seat tube, and the spray from water hitting that is the primary source of the water that gets under the saddle.