The probe detects the tone(signal) placed on the copper line and generates an audible sound. The stronger the signal is, the louder the sound will be. In telephony you usually plug the tone generator into a station cable that is in need of identification and then take the probe into the IDF. When you get to the IDF, you can run the probe up and down the rows of the 66 blocks, but that method won't always get you the results you want. An experienced telephone guy taught me to hold the probe in one hand near your ear (so you can hear it well) and then use a finger on your other hand to run down the conductors. When you hear a tone, you can isolate it by using your finger to touch only one pair of conductors. For example if the tone is coming on the blue/white cable pair you should be able to place your finger on the orange/white pair and not hear tone, but when on the blue/white you will hear tone. There is only one drawback to the finger method... phones use voltage to ring which means that if you happen to hit a ringing line, it might bite a bit.
My particular model of toner is a Fluke Networks IntelliTone which has a digital tone option. This comes in handy when there is digital phone signal or data signal on the line. Using this option is the same as the analog method, but many times it will power through noise on the line.
Sometimes phone installers will split a CAT5e cable into two jacks with blue/white and orange/white on one jack, and green/white and brown/white on the other jack. In this configuration green/white and brown/white are wired to the blue/white and orange/white pins on the jack.