Jim, those other two holes are simply to keep the seat shaped and provided support against the hull. I've got a fleet of 4 yaks and one has a seat similar to yours.
Your next project: Greenland paddle. Once you carve and use one, you'll never go back.
I just finished my second one.
http://www.qajaqusa.org/QK/makegreen2.pdf
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paul, texas KD5IVP