Decker is almost right. The key is that the info now needs to be loaded for internal flights too - so while you do submit APIS for a VS flight, which de facto covers all secure flight requirements, you don't submit it if you're booking a VX flight on a separate PNR - so you will need to do this for such a flight too.
There are at least four ways I have found for doing this with UA:
1) If you have a FF account with a given airline, you should be able to store this info as part of the account, then every rez containing you FF# will automatically pull in the info. This is how I do it
2) When you book a ticket online, you have a field where you can enter the data
3) On a "My rez" summary screen, you should have the option to do this - for UA you will see either a green check mark or a red exclamation point below the main rez detail list, with a link to review the info, which takes you to a screen where you can fill in the data
4) Call the airline and ask them to add the info to the PNR
I've no idea whether the program will help, but the idea's not that daft. For me it's a non-issue, as there is no one else in the US with my surname, but folks used to get stopped for having names that matched the list, *if they can get this to work* it should prevent such last minute hassles from happening in future.
The idea is that, if you happen to be called Mr bin Laden, one way to prevent TSA from kicking you off the plane all the time is to furnish your full and proper name (which might alone disambiguate the situation), a DOB and a redress number if you have one. A redress number is a cross-ref to communications you might have had with Homeland security about who you are, and why you should be allowed to fly. Provide the info ahead of time and you won't find yourself batting on a sticky wicket at the airport if you happen to be ticketed as O. bin Laden

And before we start thinking "they'd never be daft enough to fly on a known and listed name", let's keep in mind that folks indeed have done this, that many metaphorical bread rolls were chucked at authorities for not running stringent checks on the names, etc etc. With more stringent checks, more people run the risk of getting kicked off their flight. With this program they're trying to ensure you don't get kicked off by resolving ambiguities well ahead of your travel date.
Of course, the proof of the pudding etc etc