Do it in as clean a place as possible as even a spec of dust will cause a bubble. I tend to do it in the bathroom as this seems to be the most dust free room. Do it as soon after getting the iPad as possible so that the screen is already spotless.
Also I run the screen protector under a tap once I've exposed the first side (try not to get too much water on it to avoid getting the iPad too wet) position it as accurately as possible to an edge and use a small squeegee or edge of a credit card to smooth it down n squeeze the air/water out from under it. If you get a speck or bubble, lift it to the nearest clear bit n try again. Lots of patience should give you a blemish free protector. I'm seriously anal about these things and make sure I get it spot on every time. Once you're happy, take off the second film.