I have a 2003 TT with stereo and heater...although I put the stereo in myself. Regardless, the speakers in the rear belong just under the back seat, on the small portion of the boat that face towards the engine. 6 1/2 " speakers fit perfectly there. I put my driver-side speaker under the dash on the vertical carpet section...next to the Perfect Pass panel. Behind the carpet there may already be a cut-out for a speaker. I put my front passenger speaker under the passenger seat, next to the lock on the base of the passenger seat.
I believe the rear speaker location is consistent with factory placement, but the front may not be. Factory settings may put the front speakers in front of the driver dash and next to the passenger glove box...but I didn't have enough nerve to drill through the top of my boat. I've also seen speakers on the engine box itself...again, not enough nerve to mess with cutting the engine box.
Heater is factory installed and one hose (removable) comes out under the passenger seat, and the other again mounts to the vertical panel near the driver's feet, next to the PP panel. I believe the heater core itself is behind this panel. Comes out pretty simply with 4 screws...but it sure is tight working under the dash.
Good luck. I'm sure others have found other suitable locations.
Factory head unit placement I believe is in the glove box...I mounted mine though just under my driver side dash, to the left of the steering column. Stuck a sub next to the passenger ballast behind the passenger seat.