if its in the boot area/spare wheel well, that usually means thats its coming in through the lower tailgate, if the side window is leaking its usually the audio compartment/equipment that gets wet, feel around the rear of the sat nav unit and the bottom of the audio compartment for damp.
hi mate i dont have my amps in anymore but there is signs off water in the bottom off there and the carpet over the spare wheel is a little damp so i will investigate when weathr fairs up , cheers mate