Both sections 5.a. and 5.b. should say how a system administrator can make the limits set in either /etc/security/limits.conf or /etc/limits actually apply.
We either need some real-world examples from you, or something entirely different. From our conversation on IRC, it sounds like you're just having trouble setting up your particular system (PAM, especially), and support requests like that belong in http://forums.gentoo.org .
