RoamDog, traditional phone jacks are one big parallel circuit. A cable goes from your NID to jack A, which goes to jack B, etc. Wire one from NID to A is connected to pin X in the RJ11 AND to wire one on the cable to jack B, where it repeats. Visualize a ladder running horizontally, where the bars represent jack positions. A phone that's on hook is at high impedance, so it doesn't complete the circuit there, but a phone that's off hook is at low impedance and that's where the top and bottom rail (tip and ring) are connected.
If you use network style home-run wiring for your jacks rather than the traditional chaining, it's just like having a really short chain near your panel and really long cables going from there to the phones. So you'll need a special panel, or you'll need to make one yourself, that simply connects all the pin 1s together, and then separately connects all the pin 2s together, etc.
If this all still seems too complicated, I believe that Lowes and Home Depot both carry a little panel that does all the chaining internally, so you just connect cables from your patch panel (and from your NID) to this little daisy-chain panel.
I admit that this is a bit hard to explain in a text-only format.