Cutting a solid surface to make a overlapping junction This one is a bit tricky.

I'm building a RC submarine in Blender so that I can have it 3d printed. I want to have a removable &quot;cap&quot; so that I can have access to the electronics inside, however, to make it water tight, I want to put in a piece of rubber inside an overlapping junction. I know I can use the knife tool to cut out the cap and I solidified my sub to give it a &quot;wall&quot;, however is there an easy way to cut an overlapping junction?
I also found that when I solidify, I can't seem to select the vertices on the expanded solid. Is this by design? Is there a way to enable it?
Normal Cut
XXXXXOOOOO
XXXXXOOOOO
XXXXXOOOOO

Side A
XXXXXXXXXX
XXXXX

Side B
     OOOOO
OOOOOOOOOO

Together
XXXXXXXXXX
XXXXXOOOOO
OOOOOOOOOO

Thanks,
mj
You could use a Boolean Modifier. Though, the success of this method may depend on the topology of your mesh. It does not always give clean or desired results, but it may be worth a try.

Also you will want Solidify to be above Boolean in your modifier stack. And if you apply these modifiers, apply the Solidify first, and then apply the Boolean.

EDIT:
You could make something like this, where the selected mesh is the (already applied) Boolean target object.

If you put the selected orange edge, shown on the left, (one is extruded inward, and one extruded outward) in in the middle of the solidified wall thickness, and then preform the boolean operation, you will end up with submarine parts that will fit into each other as shown on the right.