It's hard for me to figure this out on the basis of the pictures (at least on my none-too-big monitor screen), but I think CapnMac82 may have it right. In other words, two odd things have happened here. One - Heller decided to simplify the prototypical method of securing the main and mizzen stays (not such a bad idea in 1/200 scale), by omitting the eyebolts and bullseyes (or whatever other devices were used on the real ship). Two - in a typical Hellerism, when the designers looked at the plans (probably the Musee de la Marine ones) they didn't know what they were looking at. The real stay consisted (if we're right) of a single, extremely heavy rope that started at an eyebolt in the deck on one side of the mast ahead (that is, the foremast in the case of the mainstay, and the mainmast in the case of the mizzenstay), went up through the lubber hole in the top, around the masthead, and back down to another eyebolt on the other side of the mast. The two parts of the stay were then seized together in two places - just below the top, and just aft of the preceding mast. In the eyes of somebody who didn't understand the system, that arrangement would look like two loops of rope with another, single rope connecting them. Our ancestors had more sense than that. And from the modeler's standpoint, the prototypical arrangement is simpler to rig.
The one virtue of the Heller arrangement is that, by dispensing with the eyebolts, it lets you set up those loops while you can get at the bottom of the deck. If I were doing it, I think my approach would be to make some eyebolts. It's easy. Get some copper or brass wire of an appropriate diameter (i.e., about as small as you can find). If you use brass wire, heat it over a candle to soften it. A twist drill bit makes a good mandrel. Form the eye around the drill bit and twist the ends of the wire into a pigtail. Shove both ends of the wire through the hole in the deck, spread them apart, and glue them to the bottom of the deck with superglue. Then forget about the problem till you're ready to start the rigging in earnest. When that happens, my approach would be (in the case of the mainstay) to double a length of thread (the heaviest you're using - this is one of the thickest lines in the ship) around the main masthead and seize it just below the masthead. Then seize one end to each of the eyebolts, leaving a little slack. (Just how much slack will take a little practice to establish; don't expect to get it right the first time.) Finally, seize the two parts together a second time, just aft of the foremast. The last seizing should pull the whole stay nice and tight.
It's becoming quite obvious that the rigging instructions in the kit are typical Heller - i.e., utterly worthless. (On the other hand, the photos make it clear that the detail on the plastic parts is pretty good. And I like what you've done with the deck planking.) It's equally obvious that describing this sort of thing verbally is quite a challenge. In order to rig this model without going crazy you're going to have to get hold of at least one decent book about rigging - one with a good set of diagrams. The Underhill book is outstanding, but a few decades too modern for this ship. (Underhill concentrates on merchant vessels of the late nineteenth and early twentieth centuries.) I'm inclined to think the book you need is Lees's Masting and Rigging of English Ships of War. There undoubtedly are some distinctly non-French things in it, but my guess is that if you follow that book you'll be at least 80 percent right. (That compares to about 5 percent if you follow the Heller instructions.) Harland's Seamanship in the Age of Sail goes into some detail about nationalistic differences; if you can find that one in a library it will help. But the Lees book is the one I'd recommend above all others - unless some other Forum member knows of a French counterpart to it.
It's obvious from the photos that a really nice model is under construction here. The scale is mighty small; there are limits to how much rigging most of us can handle on that scale. Some omission and simplification are just about unavoidable. But it would be a shame to do less than a good, sensible rigging job on a models that's off to such a good start.
Hope we're helping a little. Good luck.