I have the new style controller (yay).
I have it mounted under the top cross member
with the fins horizontal, and have covered the connectors
on the back side with 2 inch shrink wrap tubing.
With the fins open to air flow I have not seen the controller
get hot (but the wires from the battery and to the motor do)
In southern California we don't have to worry about rain too much
(tho we are expecting the one of the two annual rains on Wednesday to Friday)
I have considered molding a silicone cover for the connector side and
feeding the wires through a grommet in the bottom, but would rather just
not ride in the rain.