You'll have to do the best you can with the hatch, or cut out a larger one yourself. You can buy new hatches at a marine store and they'll have a template to cut from.
If you can get your arms inside the bilge, you should be able to replace the pump. The hardest part is usually the wiring. If you're going to run new wires, use the old wires to pull the new wires through to the center console (or wherever your battery/switches are). Connect the wires to the new pump before installing the new pump inside the bilge.