How do pilots of small planes know where to move people?
Depending on the airline, and the size of the aircraft, the Weight and Balance calculations for each flight are either done by the pilots, or by the Flight Operations, Load Department. 

If it is done by the pilots, they will receive the loading information which contains the weight and location of all passengers, cargo, and fuel. They then calculate manually, or by using software, the exact center of gravity. 

If done by the Load Department, the center of gravity information will be communicated by radio or ACARS datalink. 

It is not unusual to require a last minute seating or cargo change in order to ensure the aircraft is within the proper center of gravity limits for takeoff.