I have done a similar build and used a led pencil to score them in then went over it with a soldering iron/wood working tool but only to make them evident as ill be painting mine in plastic
Sorry I havent replied sooner, I just use a pencil, don't do it too heavy or you will tear the foam and it will look ugly. Draw the lines on, then go over them again a little heavier and repeat 2-3 times. You want to score the lines enough that over time the foam wont just expand and make the lines dissapear. You also want the lines to be deep enough that when painting the paint doesn't cover and fill in the lines. Hope this helps.
My next cheeky question to Familyman is.....will you be publishing the templates as jpegs or pdfs? I made a Anubis head from the Pep file but it doesn't look right. I'd be very grateful if you can.