I have a 2005 288 MCOB I am setting up a new boat lift. Do I need to make the bunks with a raised portion for the step in the back or can I use a flat bunk?

You definitely want the bunks cut to fit the exact shape/step of the hull. You can use small strips of wood tacked on top of the main bunks to adjust the height. You also want the main bunks of the lift to support the boat directly under the main stringers.