Usually just a matter of constraints on where the engineer can physically fit the fueling port with the limits that it must be an upper surface, not too near critical components that may be damaged, and have minimal aerodynamic impact. The plane must also deal with the substantial change in center of mass and angle of attack[required lift] during the fueling. All these factors vary with the design goals of each model.
The drogue and probe method is used by the US navy and most international air forces. This is a very adaptable system that can fuel multiple small planes from wing mounted hoses on one tanker or small plane to small plane, and even works with helicopters(using a very long probe); the down side is that maneuvering to couple is more difficult and each drogue design has a narrow speed range. The probe must be in located view of the pilot.
The port and flying boom method is used by the United States air force; it was developed by the strategic air command early in the cold war for strategic bombers. As such the flow rate of the flying boom is an order of magnitude larger than the hose and probe, and it can be used across a very wide speed range without changing parts, with added benefit of no probe to effect drag, radar signal, or to get damaged; the downside is the tanker can only serve one plane at a time, the port must be on an upper surface, and the tanker needs a boom operator.