I'm sorry, I should've been more clear about the differences between the project on that page and my own setup. I referenced the article as it deals with common anode LEDs instead of the seemingly easier to work with common cathode LEDs.
He's using a single 5v LED without built-in resistors. I'm using a 12v LED strip, but still common positive (in this case, common anode, correct?) with built in resistors. Can I power the Arduino with 12v via the input jack, and have the positive end of the LEDs attached to Vin, and the negative end of the LEDs attached to the pwm pins without fear of burning anything on the Arduino out?