How do I seal a new door sill from leaking?

I've been having problems with water seepage underneath both sills on a basement and exterior garage doors when it rains. How do I know if the sill was part of the original door jamb when it was installed. If it wasn't how do I remove it with minimal damage to the door jamb? Also, when i install the new sill what type of caulk should I use( acrylic+silicone, liquid nails, waterproof paneling adhesive, polyurethane, concrete+mortar, etc...) and where do I apply it?
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