I've never done down pants, but I've done a couple of jackets and a sleeping bag. I think you'd sew the quilt lines before stuffing with down (that's how you do a jacket.) Then baste the edges to keep the down in, and sew as usual. If you tried the diamond-shaped quilting pattern, I think you'd have to sew through the down. With the small amount of down required, either way ought to work.
I imagine a rain pants pattern would work OK, as long as you made it large enough to accompany the extra thickness. A slight differential cut, that is, having the shell slightly larger than the liner, might make them fit a little better, but may not be worth the trouble.
Down isn't all that hard to work with. Just work in a draft-free room, and work slowly. Figure out by trial and error how much down you need for one compartment, and use a digital postal scale that reads in grams to weigh the down for each compartment.