I've just done a count, and five of my machines have Brooks saddles. Those all have mudguards, so soaking from below isn't an issue, except perhaps on the trike, which doesn't have rear guards.
I've always applied Proofide to the bottom only. This is more to do with assuming that getting grease onto clothing would be an issue with applying it from above. Obviously I wouldn't ride straight after an application, but it sounds from what people say here as though it really does soak in completely? Looks like opinions are varied anyway about the best approach, though.
I'm not very systematic, so I tend to do it when I get the saddle, and if it looks like it needs it (which would not be anything like every six months).