I've done both. On a new vehicle with good fluid, I'd probably be inclined to just do a drain and refill. On higher mileage transmissions, or ones that show signs of bad fluid, I'll do a flush.

You can flush it yourself with a rubber hose. Just disconnect from the tranny cooler and attach a rubber hose. Direct it into a drain pan. Then start the vehicle and start adding fluid in the top while it gets pumped out below. Figure on a few gallons of ATF this way, so watch out for overflowing the drain pan.