Check out the wire frame shelf that I added to my James Baroud RTT detailed in the post referenced below. You might be able to adapt this approach to your clamshell. I had previously done something similar with some cargo netting but found the wire frame shelf worked much better
Sure-Fire Ways to Improve Your Roof Top Tent
Who all makes a shoe bag for the RTTs. The Yakima and Tepui look good. Any others? Compact camping concepts sells a shoe hammock that works pretty good. Compact camping conceptswww.expeditionportal.com