If your flow meter has three wires and is powered by 5V, then the three wires must be +5V, GND, and data (typical colors are red for +5V, black for GND, and some other color like brown for data).
On the rain sensor port, the right port is GND, the left port is DATA, and +5V is not mapped out (except on OpenSprinkler v3.0 which exposes +5V through terminal block). So you have to solder a wire onto the circuit to the VIN (which is +5V) pin.