In the WoW reputation window you can opt to show the reputation progress with a specific faction as "experience bar".
Reputation Watcher extends this functionality and changes the faction shown on this bar automatically whenever you gain reputation.
If you do not want a specific faction to be watched simply select "Move to inactive" for it in the WoW repuation window.
There are situation where you already have the highest possible number (2) of (other) experience bars shown, like xp and artifact bar when leveling in Legion or BfA. In these cases Repuation Watcher will not automatically select factions to be displayed because this would make one of the other bar's invisible (most propably the xp bar). If you still want it to work simply select "Show as Experience Bar" for any faction in the WoW reputation window which makes the bar visible and tells Repuation Watcher to do its job again starting with the next reputation gain.