From my understanding the "Mark" is just putting a layer of black junk into your etch while the "Etch" is actually removing metal.
I Etch mine to desired depth, then mark. I follow up with polishing the area with mothers mag polish, which then deposits a lot more black down into the deep etch. Looks great!
I probably do 10X about 15 second passes. I dont leave the etch on any longer to avoid burning the stencil.
Mine are etched deep enough that I'd have to grind a significant amount away before the mark would be gone. They are deep enough that I can put my fingernail down into them.