The tender port is at the bottom of a cliff. The town on top is Fira. To get up there you either take the cable car or go up a path on a donkey or by foot. Ship excursions tender to the ferry port where there is road (cars, buses) access to the island. Because of local authority deals with merchants, cable car, etc., most ship excursions have to return to the ship by dropping off the pax and then going down to the tender port by cable car or down the donkey path. Some ship excursions are allowed to drive back to the ferry port and tender back from there.
My advice is going to SB Square as soon as you board and ask about the options. Also ask about the tender for independent excursions and to which of the two ports it will take you.
Santorini is lovely - nice towns, beaches, views, Akrotiri ruins, etc.