FAF utilizes two different trueskill values or "ratings" in order to gauge player capability in two 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 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 two 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.
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