The blue washout marker leaves a line too fat for my applique. I need a very thin sharp line so I use the Frixion pens. I know that they will come back in the cold but I sew my applique piece to barely cover the line so it will never be a problem for me. Even if the line comes back, it would only appear as a framework for the stitching. I know one fabulous applique stitcher that sews a line of embroidery around every one of her pieces so the frixion faint line would look just like that.
The smaller the pieces, the thinner and finer the line needs to be. The block I'm working on now has 51 pieces in a 8" square so those are pretty small applique pieces. All these LBB blocks will be 8" square finished.
I don't mark a line on my applique pieces. If I'm overlapping something, I make a clear plastic overlay so I can line things up. And then, I leave my template piece pinned to the fabric applique piece so I can turn it under perfectly. I know my methods might not work the same for everyone. We all have to adjust and perfect our techniques. But it works for me and I keep working at getting better and better.