Thanks for the replies so far,
I tried clicking on upload using programmer and all it does is reprogram my arduino not the slave board it's connected to.
I currently have the ArduinoISP sketch installed on the arduino,
the MISO, MOSI, RESET and SCK wires from the arduino connected to my PCB,
a 10uF capacitor between the Arduino RESET and GND pin (to stop it programing the Arduino... in theory!)
Then I have Board set to Arduino and Programmer set to Arduino as ISP.
I'll just run through it all again slowly and check the output on pin 13 to see if it gives me a blink, back in 10mins (don't have a scope in my office)