I would try a pencil first, then a china marker. Make sure you can get the china marker off before you install!
I would seal before grout, and probably use a white thin set if they're white-ish tiles.
Yes, those little hex tiles are a PITA, but pretty when done.
You can sometimes buy pre cut "points", three point or four point sections that are half cuts of the tile, for starting at walls, etc.
Also, you can use a fine point sharpie and mark on the "wrong" side of the cut so the mark will be cut off.
I also use a rubber hand roller for pressing the hex sheets into the thinset.
I've laid a lot of hex, biggest thing is to go easy on the thinset so you don't get a lot of push through of the thinset when you roll them out.