By default, the Secondary track in a matte container or multi-channel clip is selected for grading.
You can select a different matte track or channel for each secondary layer of colour grading. This is useful when you want to grade the image based on the values in its colour channels. You can make this change from the Colour | Secondaries menu, rather than going into the matte container on the timeline.
Here is a matte container with 3 matte tracks, V2.1 is set as the secondary.
In the Secondaries menu, you can enable a different matte for each secondary layer. Enable a secondary. Then click the Matte button and select the matte track to apply to the secondary.
See Working with Mattes.