If the motor is already in the well, I would leave it there. Just tighten the mounting screws, although the engine can't possibly slip through the hole.

If the motor is not on the boat yet, mounting it in the water or on the hard is a little awkward either way. You either have to carry it up a ladder or step on to the floating boat carrying it in your hand.
It helps to have someone guide the lower unit so the prop doesn't ding something.

Set up a "landing pad" on the boat with boat cushions or something to put the engine temporarily until you're ready to lift it into the motor well.