there are three types of fee waivers -- one for the ssat (the waiver is good for one time only, no free retakes and it will not pay for late registration); one for the SSS form used to request financial aid and one for each school for the admission fee.
Income qualification is required -- but those of us who are low-income know that we qualify and proving it isn't hard. For my son, we simply told them that he qualified for reduced price lunch and could send them a copy of the form (no one asked for me to send it -- they just took my word).
For the SSS form and the SSAT test, you ask at just one of your prospective schools for the number. My son asked at Andover (even though he didn't end up applying there) and they were able to give him a code right away. It probably is best to ask early -- but my son didn't ask until December and still got the waiver number.
As far as an admission's waivers for each school -- you need to contact each individual school and ask them to waive the admission fee. Even schools that say on their website that the admission fee is required for all, or don't mention a fee waiver will most likely waive the fee. At some you will need a code and at others you will send in a note with the application.