Kutna Hora is two settlements 3 km apart - the medieval town on the ridge and Sedlec down by the ossuary and the main station - and choosing wrongly costs you a bus ride every time you leave the door.
The old town around Palackeho namesti
The obvious base: Sultysova, the Italian Court and the walk out along Barborska all start here, and this is the part of town that is worth having to yourself once the day tours leave for Prague.
Barborska and the upper end
The ridge above the Vrchlice valley, along the terrace to St Barbara's. Quieter than the square, with the best of the town outside the window, and a short but genuinely steep walk back up whenever you go down to the river.
Sedlec - by the ossuary and the main station
Cheaper, flatter and next to the trains, but it is a separate suburb 3 km from the old town with the ossuary, the cathedral and the town brewery for company and not much else after dark.
Two stations, and the one you want is the small one
Trains from Prague arrive at Kutna Hora hlavni nadrazi, which is in Sedlec, not in the town. Local trains carry on from there to Kutna Hora mesto, the small station below the old town. Book your bed for the station you will actually use, and check the last shuttle before you plan a late dinner.