It looks like dowel locator inserts will provide very exact results. But haven't we all replaced seats without such precision?
Crude but effective method: clamp the seat to the gunwales in the position you want it. If the gunwales are new, drill the gunwale and seat frame at the same time. If you are fitting into a canoe with existing gunwales, just take a pencil, put it through the the existing seat-mount hole, and mark the seat frame. And, it appears you have the old seat, so you could just put the old seat on top of the new seat and drill through the old seats existing holes.
I've installed a dozen or so seats in this manner. I'm thinking Robin and Boatman53 have installed way more seats than I have. It's so simple I'm thinking I must not understand the problem.