I've not tried it yet, but I have some Bestop full door jackets that I plan on using on the next trip where I remove the upper doors. I will probably cut some window-shaped pieces from a yoga mat or foam flooring for the slider windows. I'll see if I can get both halves in one jacket or have to use one jacket for each. From there I will secure the bag/jacket in either the back seat or somewhere in the bed (I have an LG, so I have a little more room back there. Bestop also makes bags for just the soft half door uppers, but I was afraid they'd be too small. I have two pairs of these Bestop jackets - one pair houses whatever doors are off the Jeep (currently my full doors) and the other pair is on standby for the uppers.
Without the jackets - maybe just try the foam or yoga mat and some bungees or light-duty ratchet straps for security. Maybe even a moving blanket any old blanket, or some towels would work too.