But if your dead set on doing it your self. The Lines come in from the Telco. and go into the CO line ports, the stations come from the Key unit to the phones. The wiring on a 50 pair block is usually wired the same, blue, orange, green, brown, slate. What or how you use the pairs depends on the system, in your case it's stations, that block will hold 12 or 8 stations all in a row. Depending on what system you have...I'm guessing it's an Onyx, DS1 modular type.

But to answer the thread title: basics of punching down wires?
Use the color code above and consult your installation manual for the station punch down locations. If your planning on cleaning up the closet, I would suggest hiring someone who's certified or has a lot of experience with your system and watch, learn what you can, most phone people will tell ya what their doing.
good luck on what ever you do.

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