Not a whole lot you can do about it. Dust is a potential issue, your best bet is to do it in the bathroom right after a hot shower. Bubbles under the protector tend to go away by themselves within a few days. Especially on the glass ones.
Yes, this is the best way. I got my amFilm on perfectly with the first pane. I first cleaned the area around my sink and put on a clean, flat surface (a USPS large flat rate box, laid unextended and flat). Closed the door and let the shower rip. The secret is to let it go until you start getting condensation on the screen - this means it's too humid - then stop the shower and wipe that away until it stops happening. That's when you want to apply the film. Most kits come with cleaning wipes but I also have my own spray for such things (1 part 70% isopropyl/rubbing alcohol, 1 part distilled water, for a total of 30-40% alcohol by volume) and either a microfiber cloth or a more absorbent paper towel like Scott shop towels. It'll evaporate quickly. Just keep sweeping as you turn the unit this way and that to catch any extra dust and once you are ready for the film, just do it in one go and don't hesitate. Bubbles are generally not a problem as long as you don't put the screen down flat all at once but more "swing" it down from one side and then push out to the corners with the included card and your fingers.