Should stove pipe be installed with the male end up or down?

Stove pipe should always be installed with the "male-end-down".

Installing the pipe male-end-down allows creosote drippings to go back down into your stove instead of running down your pipe onto the stove or floor.

(Click on the how to install your own woodstove photo for more information).
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Stove Pipe Coupling Position

install your own woodstove