The best way to get a nice seal on a hatch is to have a good plan before starting to build. This can be as simple as a hand sketch of the cross section where the wall and hatch meet, and then a couple of details about what will happen at the hinge and back edge of the floor. There are several variations that have proven to work well in the past, most of which can be incorporated in one form or another. Usually these rely on at least the outer hatch skin overlapping the edges of the galley wall.
Perhaps if you post some pictures or a sketch of what you have, you might get some more useful help and ideas.
If you have not done that and your skinned hatch is sitting inside of and flush to the profile edge of the wall, perhaps you can add another skin layer, or just an edge trim piece fixed flat to the perimeter hatch so that it overlaps the wall. You might even want to build this up with a shim to allow some space for weather stripping (or use a rabbeting bit in a router to cut a notch for the weather stripping in the outside edge of the wall). Len's method (link)
might give you some ideas on an alternate method to surface mount a seal with an inset hatch. However, you will see that the hatch skin still overlaps the seal.