Okay. The intake has 12 runners for 6 cylinders - two per. However, they only use one much of the time. The "secondary" runners are used at high RPM's, when the engine needs a ton more air flow. The "secondaries" refer to the butterflies that close off the secondary manifold runners so they don't feed the cylinders too much air when they don't need them.
The IMRC (Intake Manifold Runner Control) is the device that opens the secondary runners at the perfect instant, which is why at about 3500 RPM's, your aceleration really kicks in and the engine roars.
Does this help?