If you think you might need to alter the garment later, cut the notches OUT and leave the seam allowance intact.
Making little 1/8 inch clips where the notches are is a good suggestion.
The notches are just guides for lining up the pieces. Example: The sleeve has a single notch and a double notch. If I remember correctly, the garment front has a single notch and the garment back has a double notch.
What kind of fabric are you using?
Most markings are placed on the wrong side of the fabric so they won't show after the garment is finished.
There might be something on youtube that will give you clues.
Also, patternreview.com might have some help.