You really have a choice.
1) You can use what I do which is a piece of MDF or particle board screwed to a pair of 2X2s after being cut to width. I like to be roughly 1/16" narrower than the planned width of the tunnel of the boat. I also have supports fastened to the inside of the 2X2s so that I can clamp the boat down without having to find something else to support the jig. I leave this flat so that I don't have to work around a raised area
2) You can take some MDF or plywood and cut it to match the bottom profile and attach two pieces to the top of that. The tricky part with this is you have to make sure the jig and bottom profile are an exact match or you could end up with a twisted hull. Since Mike's kits are tongue and slot, you shouldn't have too much of that to worry about.