Fitting cleats a stupid question or not?

I have taken the plunge and bought some spd's and cleats for my MT31's. I have taken off the cleat cover on the bottom and put the cleats on, so far no problem. They even fit onto the pedals ok. The questions I have are , is there some sort of rubber seal that should go on the bottom of the sole so that water can't get into the shoe. You can see into the shoe through a small gap when the insole isn't in place.Is it me? :?
And how should you adjust the cleat to get a natural riding position?
And how should you adjust the cleat to get a natural riding position?
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Parktools :?:SheldonBrown
Ideally the plumbers-pipeseal variety rather than the bathroom edge sealant as it's easier to remove again. I fill the slots in the sole, then fit the cleats to make a completely waterproof seal.
I also fill the cleat bolts hex-key void, and the space between the cleat and the round-ended plate so that dirt and grime doesn't accumulate. When (If!) I need to remove the cleats, it's a two second job with a small pointy thing to clear the holes in preparation for removal.