I haven't done this on a roof rack, but I suppose it could work.
On my trailer, I'll have the canoe loaded and strapped people side up, then lay kayaks inside it and lash them down. I suppose it could be done on a roof rack too.
The only thing that concerns me is the weight of the items. Don't exceed your factory racks weight capacity.
- Big D
Cartop Kayak Carriers
Canoe / Kayak Anchors