Val,
What's important is that the cart posts extend all the way through the scupper and out above the deck. This ensures the strongest parts of the scupper, the top and bottom, take all the forces of the cart and not the weaker scupper tube.
The pin at the top is the keeper pin designed to ensure the cart posts don't slip down and damage the scupper tube when underway. It also holds the cart in place on the kayak making unloading from a roofrack/trailer easier.
Set the cart collars (flanges/bushings) so that there is enough clearance through the hull that the keeper pin can be inserted horizontally through the lower hole in the cart post and that the hull bottom does not hit the crossbar (prevents hull oil canning).
Roadrunners reply in this post will help:
viewtopic.php?f=11&t=14028A search for carts and balls will yield other useful info.