There shouldn't be anything mounted underneath the red circle area. It wouldn't make sense to put anything there - there's no reason to run wires or anything there. Can you see that area by looking up from the battery area or from that hole on the port side?
Are you looking for a place just to store the rods and/or light trolling? If so, no need for backing plates - just screw it in (unless that fiberglass is really thin). But if you want to use nuts/backing plates, that cushion should be removable. Cut an access hole or two and replace with a deck plate.
What's that black thing to stbd of the red circles? Remove that - that would provide another way to get a look at things.
This looks to be a pretty easy job, actually.