This is my method:
1. Clean screen with alcohol, after this is done do not touch the surface with your fingers.
2. Start to unpeal the screen protector, start at one end but do not take off the entire backing yet. Taking off the entire backing will allow dirt/dust to gather.
3. Start at either the top of the phone or bottom, if the screen protector has cut outs then I usual start with the end.
4. Align the protector and just touch a small amount to the screen so that it sticks.
5. With a credit card push the protector onto the screen while peeling off the back. Using the credit card to install the protector in this method will prevent bubbles from getting in there in the first place.
6. Once installed run the credit card over the protector a few times, specially near the edges to make sure it is seated.
I have used this method many times on my phone (and my friends) with out any issues such as air bubbles.