the rear axle has an air hose that ends directly behind the fuel intake. the front axle has an air hose that end at the right side of the radiator next to the bottle with the engine coolant(if you stand in front of the car).
the TC has an air hose that ends over the tranny under the body. i extended it that it ends next to the battery.
the 4-gear auto tranny has no air hose. if the engine runs and the tranny works there can´t get some water inside. only if the TJ stands in deep water for hours with stopped engine there will be a problem.
about the air hose of the manual tranny i don´t know anything.
if you want to go through deep water i would also seal the openings of the tranny and engine dipstick with some tape or so.