As Jorge says, pencil marks that have been put into water will be permanent.
There are a few things you can do to help this situation. The first is do not put any marks on the paper. Depending on the paper you use, you may be able to make a template of a piece of paper the same size as the paper you print on, and a piece of black construction paper the size you would like the masked area to be. Then, you lay the paper you will be printing on top, and use the black box visible through the paper to guide the location of the coating, etc.
The other way it to only put a pencil point on the paper, not a line. That way, if it is visible, it will be very insubstantial, and if light enough, may not be noticeable at all.
I don't mark the paper at all. I use a piece of matboard cut to size as a form that I measure and set on the paper in the correct location. Then, I mask around the edges of the matboard with a low-tack masking tape. Finally, I pull off the matboard, make sure the edges of the tape are down with a boning tool, and coat the paper.
Once coating is done, the masking tape is removed, and the paper is ready for exposure. No marks, and no extraneous pt/pd solution to worry about fogging or incomplete clearing.
---Michael