Three most common ways:
Pull power from the headlight bucket. This keeps you from having to run a lot of wire from the battery, and insures that when you turn the key off, your not still pulling battery power. You just can't use it when, well, the key is off.
Run it directly to the battery. You have constant power this way, so you can still use an accessory when the ignition is turned off. But you need to remember to unplug or turn off your GPS/iPod/etc. Just make sure you run an inline fuse in the wiring.
Add a separate fuse block under the seat, and run it to the battery. This allows you to wire multiple accessories through the block, with minimal connections to the battery. You can run a 12v socket, radio, GPS, LED lights, etc.. all off of one block, without pulling load from other electrical systems. Again, just remember to turn things off when you kill the ignition. You can probably also pull from the headlight, or other place so things shut down when you kill the ignition, but you have to be careful how much load your pulling from where.