6 volts is a awkward value to wire to an arduino. Wiring it to the external DC connector or Vin pin is marginally too low for the required drop out voltage for the onboard +5vdc regulator. Applying 6vdc directly to the +5v pin is right at the absolute maximum safe voltage rating for the controller chip on the board.
my only solution is to get it to 5V and power arduino via USB, but should I limit the max current via the usb?
There is already a on-board 500ma thermofuse protecting the USB power input to the board, however +6vdc is still too high to wire directly to the USB power input. The easiest way to wire +6vdc to an arduino board is to wire a series diode between the +6vdc to the arduino 5v pin, this will drop the voltage about .6vdc and be safe to directly power the boards +5vdc bus. The cathode end of the diode would wire to the arduino 5v pin. Lefty