There are lots of ways people use to keep marks on the glass while grinding.
Paint markers will stand up to a lot of water if allowed to dry before being taken to the grinder.
Covering the marker line with Vaseline or lip salve will preserve the line longer.
Sticking down a water proof pattern piece on the glass will allow grinding up to the edges of the pattern piece without it breaking down. But of course, it can be ground away or pushed aside by the grinding head.
All these methods assume that there is a lot of grinding needed.
If you cut accurately, only a small amount of grinding will be needed and permanent felt tip/marker on glass lasts long enough to do the job.