Just add a switch on the positive wire between the battery and controller. Wire your battery as follows:
Positve from battery: inline fuse. From there, splice the battery wire, black switch wire and positive wire to the charger connector. The red switch wire goes to the positive side of the power connector on the controller. You could reverse the switch wires if you want to.
Negative from battery: Black wire from the battery gets spliced to two wires. One to the negative wire to the charger connector, one to the negative side of the power connector on the controller. It doesn't matter what kind of switch you use, but if it's out in the open, a key switch is recommended so nobody could mess with it. It's a good idea to have a switch for the controller, to prevent battery drainage. It should be turned off whenever the bike isn't being used.