I don't think I'd just lay it there, even with something under it.
It might start to build up heat.
If you are going to mount the bare board in there, I would recommend using standoffs like you would use to mount it into a case.
They are basically just hollow pieces of metal that go on the back side of the mobo, around the bolts that are holding it down to the case.
Ideally, you would still want some ventilation for it though.
Can you get your entire case in on it's side?
That would let you just pull it all back out, stand it back up, and use the drives, etc... when you needed to add/modify something.
Most cases don't have anything on the right side as you look at the front.
If you set it on that side, everything but the removable drives should still work fine.
I would recommend putting a blow hole in the other side, and mounting a fan there to get the hot air out of the case more efficiently.