Frixion pens I do not recommend for marking anywhere it will be seen. You can get ghost lines on dark fabric after ironing, I like to use regular white school chalk for marking on medium and dark fabrics. Do not use coloured chalk as it can be difficult to remove. Some like the Crayola washable markers but I would test first.
If you are using rulers you can do little marking with just starting and ending points. Watch some of the YouTube videos by Angela Walters or Natalie Bonner.