Seen all the other responses. All valid places to check for leaks. however with regards to the bilge pump being on auto. It will only run when the water level is such to raise the pump float or activate the sensor. Its will then pump until water is lowered to a low level and then the pump will stop until bilge level rises again. You said you only have a couple of inches of water so there should be no problem with pump draining battery. One thing is for sure. You do NOT want water getting to a level where the starter motor and toothed flywheel (in bell housing are getting flooded!).
Two choices whilst investigating leak source. Take boat out between trips, leave pump on auto if you are genuinely only getting a couple of inches..
Little leaks can become big leaks whilst your back is turned.
As TT said, if it was me I take boat out, empty bilges completely. Dry whole bilge front to rudder post with cloth/tissue, Remove rear floor panel so you can see gland nut and rudder post, launch boat , wait and watch!