The red dipstick near the front of the engine is the sump oil. The yellow dipstick near the rear of the engine (LHS) is the auto trans fuid. Manuals don't have a dipstick - you just fill 'em up till they overflow the filler hole (located on side of trans) when parked on the flat.
You fill the auto through the dipstick hole. Use the correct fluid for the gearbox (in your manual) unless you want issues later on.