I've done two layers of batting because I wanted the extra warmth and I like the extra heaviness when I'm curled up in the quilts. I used the Hobbs 100% cotton batting, no scrim, and I don't find the two layers too thick or stiff. They are a little stiffer than a single layer, but the single layer ones are positively flimsy (I don't do dense quilting).
The quilts were all stitched in the ditch, every 3 or 4 inches. My machine handled it just fine (regular sewing machine) - it's still much thinner than hemming jeans and things like that, and my machine handles hemming jeans without balking. The extra weight makes it harder to manipulate under the machine while quilting it, but for me that was the only downside.