By stems, I assume you are referring to the threaded pipes that protrude from the bottom of the faucet. A flexible supply line should screw onto these fittings easily and you should be leak free without needing any goop or teflon tape. The other end of the supply line should connect to your copper pipe or shutoff valve, if you have one.
Perhaps you can post a photo of your leaky faucet. I'm not aware of any threads that have a flat side.