can waypoints from construction sites be automated?

[geoschmo]

No, the best you can do is way point them to the resupply depot and then when they get there, or are enroute, click them and give them additional orders to move to the second way point.

You may be able to find a planet on the path that you can build a resupply faciliity.

There is also a little thing you can do with specifying minefields to get ships to reroute so they pass over a resupply planet. Although this only works to a point. You can't get them to go way out of their normal path. Only a square or two if the alignment is right.

Geoschmo