Completely? Set opacity to 0%.
Only parts of the picture? Use the Ultra effect or Keylight in AE to make a chroma key.
If you overlay your video with other clips, there is no need to adjust opacity.
I am not sure that I understand what you want from your overlay footage.
Do you want to see the underlying Video around a portion of that overlay footage, or perhaps through "holes" that you punch in it, or do you want to "ghost" that overlay footage, so that you see the underlying footage "through" all of it?
Knowing what you wish to achieve will determine which of Harm's suggestions you will want to use.
Nice article Todd, and thank you for sharing that.