Figure length X wideth, and add teh hatches as extra. Plus include any vertical spaces. Like if you front deck goes up 16" add 16" to the length.
You could cut the hatches out of what your laying down, however then you wont be able to wrap it around the underside of the hatch or the deck. So I factor in the hatches as additional material and what you cut out as scrap or use it on a smaller hatch.
Dont forget to add in what ever you plan to wrap around the outside edges, plus a fudge factor.