There is no "special way" to hook up a phone line. In fact, there are many different color schemes that have been used over the years. Wire colors are a function of when the wires were installed and who did the installation. In other words, there is no way to know exactly which wires to use without testing.
Two cables most likely means your phone jacks are wired in a daisy chain. One of the cables feeds a jack further down the chain while the other comes from an upstream jack or from where the phone line enters the house. You should see the wires in one cable connected to the other cable, most likely on the screws of the jack you're working with.
If you're willing to do some testing on this and other jacks in your home, you should be able to figure this out. The test is simple - see which pair of wires results in a dial tone and working phone. The voltages are low, so you don't have to worry about getting hurt (unless the phone rings, which will provide a surprising shock).
If all of this sounds too difficult, an electrician or home theater installer can do the work. You could post some pictures here and we might be able to figure it out.