I've sewn for years, I always cut notches out. How I mark the fabric depends on the fabric and what I'm marking.. Most of the time I make tailor's tacks you take a couple of little stitches (I use and x) and leave loops, then when I take the pieces apart to stitch (like on darts) I snip between the layers and both are marked. Tippy
I have too. I just snip in the notches,,do not cut them out. For all other markings,take a needle and thread of a bright noticable color ( do not knot) and mark (with an X is good) leaving a tail to pull out later,
I have always found that if you are making fashion clothing that it is easier to do alterations on ready made clothing, especially if you are hard to fit.
good Luck!