The groundglass is just ground glass, and there's a fresnel lens underneath it. If your groundglass lacks markings for 645, then remove it, and mark the underside of the glass with a pencil to show where the 645 framelines should be. The glass is the same size as the format, so just hold it up, centered over the frame gate on the 645 back to trace the lines. You can mark the whole frame or just the corners, if the lines interfere with your 6x6 composition.
The frame that holds down the groundglass is held in place by 4 screws. When you remove it, note the orientation of the groundglass and the fresnel. The glass should be frosted side down. I don't recall offhand which way the fresnel goes and sold my S2As some years ago.
If you haven't already done so, now would be a good time to clean the fresnel and the groundglass before marking them, and replacing the foam under the frame. The old neoprene foam tends to deteriorate and pull up on the groundglass, causing focus problems. Clean it all off. Naphtha is a good solvent for that. You can replace it with more neoprene light seal material (or just cut up an old mouse pad), or use Moleskin, of the sort you put on foot blisters, which won't break down as readily. As I recall, I had one layer of Moleskin on two sides of the frame, and two layers on the other, but test and figure out what works.