How do you protect the underside of your brooks leather saddle?
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.