Lipets,
It's nice that you want to protect your cycles. Storing them on the inside of a compartment can be a bit of a challenge due to irregular shapes and sizes of them. To actually "build" a mount for them, to me would be fun, I used to do that for an "off duty" assignment on the FD. However, if you don't have any back ground in fabrication, or alteration, construction, modification etc. of tool mounting, compartment organization (truck bed tool boxes etc.) and that sort of thing, it would be a bit hard to create just what you need/want. Keep in mind, you're going to use up a ton of physical space, just with two bicycles.
Home Depot, Lowes, and local hardware stores many times have tool clips for things like shovel handles etc. that are spring loaded to "capture" round handled objects and hold them in place, either for stationary mounting or mobile (in trucks, motor homes etc.). What might be needed is some, what I would call stanchions (items made from wood, plastic, metal etc. that would raise the tool clip off the floor of the tray etc). so the bike frame would be sort of "suspended" but, held in place. Only about two, possibly three of those would be needed for the mounting of one bike.
The problem is the handle bars. They are wide and take up a lot of dimension. You'd have to account for that and just allow space for two of them, due to the fact that you have two bikes. If you take a look at a couple of the pics I'm sending along, maybe you'll get some ideas on what you'd like. Just few thoughts here partner. Good luck.
Scott