FAF utilizes three different trueskill values or "ratings" in order to gauge player capability in three different environments. There is the ladder rating which is meant to showcase your ability in the controlled environment of the 1v1 matchmaker. There is also the matchmaker rating which is meant to showcase your ability in the controlled environment of the 2v2 matchmaker. Finally, there is the global rating which is meant to reflect your ability to play ranked custom games. Ranked custom games could span a wide array of game types from 1v1 to 8v8 and can even include certain ranked mods such as Equilibrium.
These ratings are mutually exclusive and so they do not interact with one another. Playing ladder will not result in you losing or gaining global rating, nor will playing 1v1 custom games have an influence on your ladder rating.
However, it should be noted your global rating CAN impact your initial matchmaker rating when you first start playing it. To learn more about this, please look at problem 2 in this FAQ answer:
You can keep track of your ratings by right clicking on your name in the client and hitting "show user info" or by simply using the website: https://www.faforever.com/competitive/leaderboards/1v1
Updated to include 2v2 matchmaker rating.