Open the palette manager from the launcher by right clicking the options button
Set up your palettes (you can set up to 10 different palettes)
Load any palette from the game using the command /palette n, where n is a number between 0 and 9, they match the palettes selection in the palette manager.
The palette will be instantly loaded in game, however there is one more step you must complete at this point (the next step might be removed in the future, but gotta deal with it for now).
Browse for the customization menu: F12 > Customization
Change any palette setting here and exit, this will trigger the server side palette saving, and you will be good to go