I have a couple of suggestions for marking notches. The first is: after you cut out your pattern piece, then go back and make a small snip through both layers of the fabric and the pattern tissue inside the seam allowance at each notch.
Another suggestion for marking your notches is to first cut out all of your notches from the pattern pieces. Fold your fabric so that right sides are together. Next lay and pin your pattern pieces onto the fabric according the layout suggestions on your pattern instruction sheet. Then when cutting out each piece, cut straight across on the fabric cutting line. Then place a dot on both sides of the fabric (wrong sides) with a fabric marking pen in a contrasting color where each cut-out notch is.