Owning a humidor is a great way to preserve the flavor of your cigars and prolong their life. Here are a few steps to follow when preparing a new humidor for storing cigars.

[edit] Steps

Calibrate your hygrometer (instructions for hygrometers vary, so check yours)
Completely saturate the humidifier in distilled water for about 30 minutes.
Dry off the surface of the humidifier and place it on a towel to drain the excess water. Return the humidifier to the humidor.
Place a shot glass full of distilled water in the humidor.
Close the lid to the humidor.
Check the level of distilled water in the shot glass every few hours. If the level decreases significantly, refill the glass.
Repeat steps 4-6 until the distilled water level stays the same.
Your humidor is now ready to store your cigars.

[edit] Tips

Periodically check the humidity level. Cigar experts generally accept 60-70% as a good range, but it is entirely up to you and how you like your cigars. Add distilled water (or a store-bought glycol solution) to your humidifier if it is too low.
Store the humidor in a climate controlled area (around room temperature). If the temperature or the humidity gets too high inside the humidor, a fungus, mold, or infestation of lacioderma can develop. If you notice any of these you should immediately remove the affected cigars and destroy them.
Some molds can be wiped off of your cigars.
Some cigars can transfer flavor/aroma qualities to one another while in your humidor, so try to keep similar cigars grouped together.