Here's how i fitted the panels.
If i understand you question correctly, it is this part that your interested in: :
Here's the outer sill, 3rd layer of the left side of the car. Left is under the door, right side of the pic is toward the rear wheel. (the 2 oblong holes here is an Erik idea to prevent water pooling in this corner)
Here is the same point on the car (left hand side), but now with the QP repair panel in place looking to the rear. Note how flush (at my hand with ruler) the QP panel sits? The QP has a 90 degree edge coming from Walloth&Neesh, which I ground down at the bottom to let the QP panel sit flush with the part under the door. Easy going 0,5 mm trial and error fitting. 20 times to get it right (enough for me).
in this pic you can see how i trimmed the leading edge, on the bottom, of the QP. It just has a 2 or 3mm edge left that is in a 90 degree contact to the outer sill. Towards the top of the QP panel, the flange still needs to be folded over to 180 degrees, but that happened later on.
the opening that you mention in your point 2 indeed exists. here it is in my car with the panels in place. On final assembly, I glued a few of the joints that I didn't want to weld, and i glued this edge shut as well: left side of pic, you can see bare metal with black glue (almost not visible, as it's black glue in a tight gap)
In the front of the outer sill I closed it as well with glue:
end of sill looks like this:
Topic form a few posts back:
Here's an option to be able to inject wax into the rear end of the sill. as there are up to 7 layers of steel in some places, i though it would be good to create this opening that is accessible when lifting the rear seats. The point of the pencil is sticking into the underside of the rear seat cushions. It'll be covered with the original 20mm white plugs. Not original, but an improvement in my view.