If you use a white layer as a track matte you have two options, Luma Matte or Alpha Matte. You can invert either of those.
If you choose Alpha Matte and you lower opacity then the layer below will become more or less transparent. The color of the layer below will not be affected in any way unless there are other layers below and you are using blend modes.
The same thing applies to a Luma Matte. Set the opacity of the white solid used as a track matte to 50% and the alpha channel of the layer below will become 50% transparent and the alpha channel will be 50% gray (.5 when checked in the Info Panel if it is set to decimal or 128 if set to 8-bit, or 512 if set to 10-bit, or 16384 if set to 16-bit). I keep my Info Panel set to decimal because I usually work in 32-bit or 16-bit comps and the numbers are easier to understand.
Check the Alpha Channel in the Comp Panel. If you are still confused please select the layer used as a track matte and the layer below, press 'uu' to reveal all modified properties, take a screenshot and drag it to the reply field in the forum so we can see what you are seeing. If dragging doesn't work use the toolbar.