Maruf, here's two of Mr. Chickadee's videos
https://youtu.be/YBhgge17vw4 and
about setting foundation stones and scribing to them. The second one shows setting the stone in more detail, I think. It's slightly different size than your boulders, but seems like a stable footing.
In both cases he's putting the timber in place to scribe it. His posts are just vertical/plumb and easy to locate without being assembled first.
I could imagine two scenarios for you: doing the same... directly scribing to the assembled frame requires raising it twice, once to scribe and once again to erect the building. Or, an indirect method of making a negative cast (mold) of BOTH stones in relation to each other(connected by a board?), then a positive cast (again maintaining the relationship/connected) that you could use to scribe the posts to while laying on the ground. The second method seems like a lot of extra work and materials. You will already need a way to raise and brace your bents while you erect the structure, so why not use it for scribing as well.
I'm not sure how "heavy" your load is? a water tank? sleeping loft?