Sound production, like video production, is an imperfect science. The true nature of sound and color is not fixed in the world because it is determined by perception. To compensate for this and adjust to a situation they include features so that those in post-production have a reference. In video production the director of photography and director will often request that a gray card be held in front of the lens so that the colorist can see what the nature of gray and black is in that situation. In a similar way the alignment tone is used to set a reference point.
Setting Alignment Tone
The alignment tone is set during the production of audio so that calibration has a reference. When you get the audio track, or series of tracks, in you can go to the alignment tone that you set so that you have a general idea of the volume and quality of the audio that you have recorded. When you begin inputting the audio to your post-production workflow you will find that the alignment tone will add the consistency you need so you can alter the tracks against what the alignment tone should indicate.
If the alignment tone is not used then all pieces of audio equipment in the audio chain will have problems. The alignment tone set on one device will set the sound through to the other devices. If the alignment tone is not set then it will be impossible to note if there are any problems in the audio chain. For example, if you are utilizing a pre-amp and utilize the alignment tone you will be able to note if there are any problems with either piece of equipment. What this does importantly on set is allow the audio mixer to adjust the levels so that the metering will be correct. The alignment tone comes in at a specific meter reading so this will allow the audio mixer to have a clear understanding of how the sound they are hearing is read by the audio equipment. If you are using older tape formats, like the DAT, then the alignment tone is going to indicate the quality of the tape. If the tape has even the most subtle problems you will be able to compare the reading of the alignment tone to what the standard reading of the alignment tone should be.
Once you are in audio post-production you can input the audio tracks and utilize the alignment tone first. You can then set the audio levels in post-production so that the alignment tone comes in according to proper readings. Those changes should then be equally applied to the rest of the audio tracks. Since the alignment tone was used for reference calibration you should be able to properly adjust all the audio tracks by adjusting the alignment tone to match the readings that you want.
Alignment Tone on Set
Often times audio recording devices will have their own alignment tone that you can use by pressing a certain button. This usually will create an alignment tone that you will want to set for -20 db.