Way points

Yes. At the location you want as a waypont, use CTRL+# (where # = 0 to 9) to set one. In a Construction Queue's settings, you can then set ships to move their automatically when constructed.

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Space Empires Depot | SE:V Balance Mod

Is there a way to unset them yet?

SEV, more than a feeling.

Set them elsewhere... A big question is how you can find them once you placed them. Also they are really useful for battle line rally points: if you change the waypoint emplacement, the ships going to the waypoint will change their course for the new emplacement.