I do use Frixion pens to trace the shapes on the background fabric for these. For some applique projects, I trace the applique pieces and not the background. I'm very careful to cover the trace marks because Frixion markings will come back when 'cold'. You don't want to ship a quilt to someone or some show in the winter and have the marks come back to life. I make sure and cover them.
The embellishments on the latest flowers are embroidery but some of them I use pigma pens. I also color areas with inktense pencils and fabric medium or white Elmer's paint pens. Learning the embellishing has been trial and error but I've had a lot of good quilters give me ideas and I'm so thankful to them.