Most road wheel bags dont work. Only a few will work with the tyres down.
I have tried every wheel bag in my garage - which is about 10 pairs - and only one set works with the tyres still up...
Mavic make a square wheel-bag. They are the ones to find. I think you can get them on-line at one of the usual venues.
I did wonder about getting some made though - and also wondered why some cleever soul hadnt dont that before? Not even a company like Stans, or Niner have thought about it.
Could always make them myself I suppose out of some tough cotton or recycled demin.