Depends on the aircraft, crew, and conditions. Both can be done either way.
In the 744 it is most common to fly with autothrust when the autopilot is engaged. In the past, we were taught to disengage autothrust when flying manually, but that has changed over the years. I see more new 744 pilots using autothrust to the flare.
It is more common to engage the autopilot on a missed approach.