Pencil marks work for me - I greatly prefer them over the alignment pins.
With stock that thick, you will want to use multiple dominos. The only really tricky part is getting the spacing between them consistent on both pieces. The thing o remember is that the centerline of the cutter is 10mm above the bottom of the fence the cutter emerges from. So if you want your mortise say 15 mm from the face of the board, the adjustable fence should be set at 25mm. A pencil line for this isn't absolutely necessary, but can warn you of potential problems if the tool isn't positioned right or if the stock isn't square.
If you are having problems fitting multiple mortises, cut one for a tight fit and adjust the tool to leave a little slack in the first one.
As with most things, it helps to try it on scrap wood first!