Dan - here's a visual of the Golite Ultra quilt on top of a GG thinlight (1/8") on top of a Neoair from a trip this weekend. They're all separate layers, and everything stayed put just fine all night. Both the Ultra and the Neoair are the short versions. What can I say? I'm only 5'3".
I did eventually put the quilt into a MB bivy, because I'm such a thrasher that I was getting cold from the sides. Another thing I could have done was berm up the sides of the Gatewood with snow so the breeze couldn't get in along the bottom edges. By the way, that Neoair is one comfy invention!
Another setup I tried at home but didn't use was slipping the quilt straps over the 2 pads and just leaving the bottom half of the quilt loose on top of them. That's all you can really do, anyway, because as you say, they don't fit inside the quilt. This also works well.