My project uses a PIR to activate a 12v car washer motor. The circuit below and sketch all works fine but only if I plug in both the USB to the computer and the DC jack to a 12v wall-wart.
The project now needs to be independant so ideally needs a single rechargeable battery to supply all power. Can I do this with a single battery and if so do I need to make changes to my circuit?
If you are using the Diceimila you need to change over the links to switch the power between the USB and the external Vin. These are close to the input jack. It sounds like you haven't done this.
In that case it should work when you connect up your 12v (and ground) without the USB being connected.
Do a test where you upload the blinking LED. Now disconnect the USB and connect the 12V to Vin. The LED should start to blink showing the sketch is running. If not you have something wrong with your power supply or your wiring up of it.