Put two 6v batteries in series, with the junction terminal to the CT.

 

No, you're looking AT a center tap transformer. Just make a connection where the purple mark is on the drawing of the secondary windings and THAT is the center tap. See? It's in the center of the windings!

And you have to use it. Connect a wire from the center of the output windings (the purple mark) to that place on the circuit board marked, "CT". You will have to use a piece of wire to connect the center tap of the transformer to the place marked, "CT". It should be about 16 or 15 gauge wire. (Somebody translate that into British for me.)

Or you can go look for a center tapped transformer with the wire already attached.

so basically join the 2 middle connections which on the diagram is purple with some wire then join another bit of wire to that "purple" wire and to the board where marked CT?

 

you lost me on the capacitor filtering

The circuit indicates capacitors are present after the rectified AC input which will raise the DC to ~9vdc.
So if using batteries they would need to be 9v.
Max.

 

When you rectify a 6V AC source and place a "large" capacitor between the positive terminal and ground, the voltage on that capacitor will be close to the peak voltage of the AC sine wave (less 2 diode drops). The peak is 1.41X the RMS value, which is what is usually quoted for an AC voltage.

Gaaa, should've updated before answering.