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The standard for guitar stomp boxes is to use a 2.1mm female DC input jack with center negative.
Take a look here to see how to set things up so you have battery and DC in power, with switching out the battery when the DC jack is inserted.
Reverse polarity protection
This is always a good thing to do for your DIY effects. There are a variety of options:
- diode on the+V supply side;
- diode across the +v/GND rails;
- the best approach: use a mosfet
SparkFun make a proto PCB for making guitar effects pedals. They also have a page with some great information on DIY guitar pedals.