The most important thing to keep in mind when applying these films is to ensure that the screens are extremely clean and free of any dust.

If there is even a tiny piece of dust on the screen, it will show up when you apply the screen protectors, and will surely annoy you to no ends.
Another thing to keep in mind is to make sure you have the top and bottom screen protectors sorted out before applying them.

For the NDSi, the two screen sizes are different, so make sure you know which is which.