Except on connector CH4-5-6 where you should never connect any supply voltage (they are all three pins for input signals to the processor) without risking damage to the processor of the flight controller, you can connect power to any other connector since the grounds and positives of all other connectors are all connected to each other.
Normally the power supply voltage is carried to the CH1 connector on the flight controller by the ESC's Throttle wire, which has the ESC's internal BEC voltage on the positive and negative wires.
In Nitro, Gasser, Turbine models where a servo is normally connected to the CH1 connector instead, power for a BEC or a 2S Lipo (with sufficient "C" discharge) is connected to the CH2 connector if not used for other purposes or to a "Y" splitter lead connected to any other flight controller connector (except CH4-5-6).
Power supply to the flight controller and servos could also be made to free pins on the receiver which is then connected to the flight controller but we do not recommend this type of connection because there would be three connections with their three contact resistances which could cause voltage drops when the servos move and draw current.