So you should have a earth wire running from the water main to the fusebox, then a separate wire running from the gas, and or oil to the fuse box.
Not necessarily. You are permitted to use one conductor to connect to both pipes.
However, to the OP, I am a bit concerned: if the wire from the water pipe connects to the gas and does not go back to the MET, then that is wrong.
For PEB's, you cannot use pipework as the conductor.