In regular service, only those in recruiting or training roles wear the green or maroon lid (if qualled, and not RM or Para Regt) when not attached to Airborne or Commando units. Other than that they wear the beret of the regt/Corps they are serving with. So RE is dark blue, not black.
However if your CoC is happy for you to wear different then it is your call, personally i would choose the dark blue, you have the qual badges to show what you have achieved, but upto you.
As for the dettol badge, my mate was ex RM, and some officer told him to put his dagger up on his arm, he refused for the reasons put above, he had qualified as a RM Commando not an All Arms Commando.