These represent a sampling of most of the pens I have used for making notations on the thin paper used to print Bibles. They are a fountain pen with red ink and an extra fine point, a dry mark pencil, a 0.2mm crafter's pen, and a red ballpoint.
Step 1: The Problem
This is a page from a Bible I use often. The paper is so thin that a faint image of the factory print from the other side of the page is almost legible. Although I did not make any notations on this page, I did highlight some cross reference listings with a yellow dry marker pencil. A dry marker pencil is good for highlighting, but useless for making one's own notations. Dry marker pencils come in quite a variety of colors. They need frequent sharpening, but there is no danger they will go through the paper.
Step 2: Bleed through
I have been using this copy of the Greek New Testament over the last 45 years. It contains markings from a wide variety of pens. This page shows markings from two pens that bled through the paper. Look to the right of the numeral 8. You can see "NB" (Nota Bene = pay close attention, Important!) in reverse from the other side of the paper. It was made with a fine point fountain pen, but that pen put too much ink onto the paper for marking Bible paper, and it bled through. Notice the red "5-6" below the "NB." For a while I used cheap red ballpoint pens for Bible marking. Within a few years the ink took on an oily look and bled through the paper, even though it looked fine for a while. I quit buying those cheap red pens. The red ballpoint in the Introduction is a pretty good pen, much better than the cheap ones I used years ago.