"The board can operate on an external supply of 6 to 20 volts. If supplied with less than 7V, however, the 5V pin may supply less than five volts and the board may be unstable. If using more than 12V, the voltage regulator may overheat and damage the board. The recommended range is 7 to 12 volts."
I've found that using 9V works well. You can simply connect the + end of your battery to Arduino Vin and the - end to Arduino ground (fig 1). You should see the green light on the Arduino turn on to indicate that it is powered.
It's also a good idea to attach a toggle switch in series with this battery so that you can turn your Arduino off and on. As shown in the images above, solder a toggle switch to the red lead from the 9V battery connector. Connect the black lead from the battery connector to one of the Arduino's ground pins, and connect the lead from the toggle switch to Arduino's Vin pin. Snap a battery to the connector. Now your Arduino will turn on when the switch is closed and turn off when it is open (figs 5 and 6).



































Visit Our Store »
Go Pro Today »




http://www.browndoggadgets.com/store/accessories/9v-to-2-1mm-dc-jack/
Makes things far easier and way less complicated.
The way your write up is worded it just seems as if you've got your Arduino powered up by this method at all times for some odd reason. Which makes no sense and seems overly complicated.
Now that you've placed it in context with a larger project when you wish to keep the USB port flush with your case, everything falls into place.
Maybe you could go back into your write up and add a paragraph explaining WHY you've chosen to do this method and put in a picture of your box.