Hi,
the trains are running via the old panoramic line on the mountains.
They are currently reschedule the timetable of the trains. You have to wait the new timetable to be able to reserve a seat.
Other possibility is to use swiss trains to Lugano or Chiasso (IC and EC) and from there RE trains to Milano Centrale. In Switzerland reservations are optional (and except tourist and travelerns to Italy that do not know this, no one does reservations) and RE trains can't be reserved, just hop on the train and find a free seat.