the inlet should be at the top, higher then the outlet if possible. I have a sccop for water pick up as well and have a valve/tap to stop the water flow into the live bait tank when I don't want it
Maybe use a jigsaw to cut the section out as long as there is nothing the blade will hit. Use a drill to create the corners then cut the straight lines. Watch the sparks when using an angle grinder. They can damage the paint or worse if close to fuel lines.
Cheers
Nick