New to drywall

you should be able to just work from the top down with the visible stud and or course use the edges of the boards for the other

pencil marks are fine, ink pen isn't unless you want to seal them all before painting.

make sure they are light. You can also erase them before painting

Pencil marks are fine, I will usually mark the field with a pencil using a level, I hate missing studs when screwing off boards. I too will write measurements on the wall.

Assuming you will be mudding and then priming followed by two coats of paint, I do it all the time and it's never been a problem.

DO NOT EVER use a permanent marker ! it will bleed through 10 layers of paint, and keep going. ask my how i know.

Obviously, rollerball pen ink is bad too. I don't remember how it happened, but I ended up with a large ink pen splatter on the face of an unpainted wall, while re-rocking my buddy's bathroom. I suggested sealing it with Gardz or similar, but he ignored me. Two coats of paint later, he went and bought the primer.