Actually a paddling friend made the same mistake and just cut out a smooth rounded opening behind the cockpit and filled it with dark horizontal strips. You don't have to do a recess unless you really want to since the boat is low enough. Maybe I can get him to post a pic. It ended up with a cockpit with a rounded dark accent shape behind the cockpit and really looked nice.

Depending where you ran short, (front or back) you could do the same.

The cockpit opening and coaming lip are a much more dominate a shape and will over power any visual thing like that as well.