There's a lot of information on the forum about cutting the notch for your hatch. There are some who elect to cut it out before attaching their walls and some who cut the notch after the walls are attached to the floor. And. as Steve said, some do not need or want a notch. It all depends on how you design it to work. If you notch it, its a critical cut that is not easily altered later. I'm not sure anyone can give you exact instructions on your own individual build.
Personally, I notched my hatch after the walls were up and the roof skinned. That way I new exactly where my hatch spar would be located (used 2x2 red oak for that spar to provide a really solid attachment point for the hatch) and I also knew the exact location of the floor. I cut the notch 3/8" inch deep using a router with a flush trim bit to keep the edges nice and square. This turned out to be quite quick & easy to do time wise, but, it was really nerve wracking because you could not turn back once the cut was started. It did require a lot of planning time for me because of my lack of experience in this area. It seals pretty well, but, actually, I think a notch depth of 1/4" would have been plenty. The notch will usually run from the back edge of your hatch spar all the way down to your floor. I would suggest you don't get in a hurry on this one and draw it out to scale on paper or in your computer software. Keep searching the forum for photos and applicable threads and you'll come up with your own plan of action.
Mike
Here's a photo of the top part of the notch and galley hinge:
