If you'd like to ship your product together with P2, but containing custom set of update sites in "Help -> Install New Software", then:
1. Go to "Help -> Install New Software -> Manage Sites"
2. Shape the list using Add/Remove/Modify, and press "OK" when you're done
3. Copy org.eclipse.equinox.p2.artifact.repository.prefs and org.eclipse.equinox.p2.metadata.repository.prefs from eclipse/configuration/.settings/
to your final build configuration directory
By default Eclipse comes with two sites configured this way - linking to ganymede release train and updates.