The body is not in the bay - the GPS guy said that the boat was the last point they could get to from land and that the other points were 7ish miles out and the GPS signal was lost after that.
Dexter didn’t plant his blood slide case in Doake’s trunk. Doakes broke into Dexter’s apartment and stole the slides, taking them to an old acquaintance to be analysed.
On his return he was arrested, the slides in his trunk then being taken into evidence.