To align the keel tubes John drills the holes in the center of the boat, this is easy to find since it is simply the middle of the king plank and the middle of the two keel planks. Then to align them so they are straight he placed a metal ruler along the two keel bolts or if a flat plate along the plate. Then look at where the end meets the transom. It should be off center by half the amount as the bolts/keel are thick.
John does this on both sides to make sure it is centered. Once the bottom is aligned he tacks it in place with CA, then verify the alignment at the deck the same way.
S45 Construction | John Fisher -- keel tubes
Photo sequence showing how John Fisher made his keel tubes. He was mounting a keel from CPM (David Ramos) with longer keel bolts so they will go through the deck when finished. He coated the brass rod with carnuba wax as a mold release.