Having thought about this a little, I think a slightly more cautious approach might be best especially connecting an electronic device to a motorcycle battery. Ideally, you should have a fuse between the battery and the DC-DC converter (DDC). I would then connect the DDC inputs to the 6V supply but leave the two output disconnected for the time being. First check is to make sure you get 12V output between the leads from the DDC using a voltmeter. I would then measure the voltage at each output lead relative to the ground at the battery. If the two outputs are isolated then you should measure arbitrary voltages; that is, one output shouldn't be a 0V and the other shouldn't be at 12V. If they are, the outputs aren't isolated and the DDC won't work in your circuit. If they appear to be isolated, with the voltmeter leads connected to the output leads of the DDC, I would gingerly touch the -ve output to ground to see whether the other output gives you +12V. If it does then your circuit should be ok.