It's been ages since I played GNB2, but I think the system is the same as GNB3 which I play every now and then.
To unload transports put the last waypoint on top of the cross of the base where you want them to. Do it with maximum zoom.
And yes, US forces reload fuel at Espiritu Santo. It's a port, not only an airfield. Order your TF to return to base and it will make way for Espiritu Santo. When TF reaches the base, all ships are docked and you can refuel them (also repair, or load troops and/or supplies).
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