I have also just started the "Whimsical Garden" blocks and I personally like the vinyl overlay method. I've used this method on two other needle-turn applique tops. It helps me position each piece in the proper place. I tried once to do without the overlay and just "eyeball" placement, but it never looked right and I abandoned that project.
One tip to keep the markings from rubbing off the vinyl is to keep a piece of paper over the side you drew on when storing. I use the paper that comes on the roll with the vinyl, just cut to the same size as my pattern. The markings don't smudge or rub off with the paper next to them.