Basically you connect to whatever you are tracing (in this case it would be the flying leads of say a window. Turn the base unit on, then take the inductive "wand" and trace over the bundle of cables in your homerun location. The closer you get to the correct one the louder the buzzing signal from the wand will be, until you quickly find the correct cable.
Once the wiring is labeled you will want to do two checks, both which will require a multimeter to measure resistance. First strip back the wiring insulation on all the wiring leads. Make sure that the cable you are going to test has no leads touching each other on either end of the cable. Then set your multimeter on the highest resistance scale possible (if your meter "autoscales" skip this step). Then measure between each cable in its own bundle (for instance in the bundle with only a single pair, you would measure between those two wires. In a two pair bundle you would measure between each possible combination of wires in that bundle.
You want to make sure that the meter reads "infinite" or the same as when you have nothing connected to the meter's leads. This will insure that no short exists between wires in a bundle.
Next you want to insure there is "continuity" between each cable. The easiest way to do this is to use a small wire jumper clip and clip between each lead to say a common lead in the bundle. For instance if you have a yellow, green, black, and red color wires in a bundle, put the first clip on the black then the other clip on the red. Then go to the other end of the cable and measure between the black and red wire with your meter on the lowest resistance setting possible (again, the autoscale comment). You want to see a near zero reading. The reading will not be exactly zero because there is a few ohms resistance in the wire itself. A reading over five ohms though, would be an item of concern unless the cable is extremely long (I'm guessing over 500 feet).
This step will take up some time, but it could save you a lot of frustration when trying to make all the other items work.