a diagram would help me if you could point me towards one.
I was under the impression that my mega 2560 which im learning about was suitable for 12 volts...or does this only apply to the input voltage.
I think you should be fine with using a 5v output from the Arduino, running that to the switch, and having a return directly to the input pin. You will want to use a pull-up or -down resistor to hold the voltage to a steady on or off so that noise picked up by the wire isn't seen as a the switch opening or closing. If the switch is normally open, then have a pull-down resistor so that when the switch is open, the input is held at 0 volts.
The circuit I described is this:
That is if 5v doesn't work for some reason, but I believe it should. The capacitor isn't necessary because you don't need to smooth an an/off signal, but I got used to putting them there on the projects I've done that used a variable DC input and didn't notice I'd put it there till after I looked at the preview.
The 12v is only the power supply. The actual inputs to the chip (and possibly the whole chip) will be damaged if you apply more than 5v to them. I accidentally put a pull down resistor to the power rail on my breadboard (12v) and it just took out one pin, but since you have one where you can't replace the chip, I would be very careful.