Using the SteriPEN is really simple. I filled a 750ml Nalgene bottle with tap water in Peru. Insert the SteriPEN and press the button (which will treat 1 liter). Swirl around the SteriPEN, stirring the water a bit until the light turns off. That's it, you're done.
Be sure to either 1) prevent untreated water from contacting the lid or rim of the bottle, or 2) lightly connect the lid and let treated water drizzle out to rinse any potential contaminated water.