I use a figure-eight loop. Fairly easy to remove when you need to. Also gives the possibility to descend on one or two ends of the rope if the middle is brought to your anchor.
Edit1: Of course not to permanently damage your core, it is advised to regularly (eg after each trip) take out the knot. This way the core gets a chance to recover.
Edit2: I strongly advise against marking the middle of your rope with a permanent marker. This for the simple reason that when you have to cut your rope, the "middle"-marking will still be there. When you have multiple middle-markings it will be hard to know which one really marks the middle when you need it.