The answer is that it slides into a small compartment in the bulkhead. The dashed line on this illustration of the bulkhead behind the pilots shows approximately where the lower side of the compartment is.
Alan Weber provided a picture of an S2F cockpit display that shows the compartment the hatches slid into.
Note that because of the length of the passageway between the cockpit and crew compartment, the aft end of the hatch hole cannot be seen in the crew compartment.*
S2F-1 Radar Crew Position
http://a4-alley.x90x.net/models/Walkarounds/Tracker.html) and used with his permission:
And in response to another question, the overhead windows were tinted green, although I don't know when that practice began. (The hatches were solid initially.) Alan Weber, who worked on civil S2Fs used for fire fighting: "in fact I never saw one first hand that wasn’t. We had stacks of them in our parts room and they all were tinted green."
* In the utility conversions where the equipment was removed and the seats mounted facing rearward more towards the cockpit, the hatch compartments were usually covered with interior quilting. In this case, the right side is uncovered.