There actually is a “not too crazy” way to mark all your scenes from within Prelude but you have to be working outside of the camera card format. Say you come across a clip that has two good takes on it, mark the first one then right click and reveal in finder, then option drag that clip to make a copy and it will show right up in Prelude next to the original, mark the second take and move on.
I’ve found that if you duplicate a clip from inside the camera card structure (MXF anyway) the original and the duplicate both disappear from Prelude’s view.