A two-line telephone, or two phones connected with a line splitter, can connect to two separate phone lines on one phone jack. Red and green are line one, yellow and black are line two. Assuming you don't have two separate phone lines, just connect green to green, red to red, and leave the yellow and black alone.
Maybe I can help to clear this up a little bit, doing lots of wiring for phones and data myself.
This whole paragraph is pretty insignificant as to your situation but it should provide a little bit of an idea on how the lines can work..:
First off- the phone company has a line that comes into the building. Through that line, there can be any number of individual wires. To have an operational phone line, you need 2 wires connected which the phone company are sending the primary number through. An example would be that they use a beefy outdoor rated version of a Cat5e or Cat6 cable. These are single cables which sheath 8 paired and color coded wires inside. A typical Cat5 would be Blue/White with Blue stripes, and the same for orange, green and brown. Because they have 4 pairs, you can technically run 4 phone numbers on that whole cable, but you have to either have one phone capable of swapping between lines, or you have to just connect the correct phone for a line for maybe a different phone number in different rooms.
Now, your situation:
I assume that by taking the cover off the phone jack, you are referring to taking it off of the old, existing jack? I can't easily tell you how to solve which colors are the main line, but if you can find where the phone line comes into your home, there will typically be a box that has a telephone line coming out that goes to your phone jacks. If you can find that box and open it, then you should be able to diagnose which wires are hooked up. If you only have 1 line, there's a good chance that only 2 wires will be hooked up, which would be the line that you need to concern yourself with hooking up to the phone jack inside. The instructions that came with the jack should tell you what the order is of the connection. I typically work with bulk quantities, so there's a pretty good chance that what I were to tell you to hook up, would be vastly different from your situation.
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