Is there a way to remove the small 1 or 2 boxes above the main icon that show cooldowns? I can tick the "Show as Off GCD" for that abilitybox and they disappear, but then the ability appears in the main rotation which I want to avoid. I basically want to blacklist an ability (Ironskin Brew) so it appears nowhere as I decide when to use it or not.

Until such option is added on a per-ability basis, it is not possible.
Considering Brewmaster is not supported coming into SL yet, I'm closing the issue.