I would actually think that's the preferred way of installing the bed wood. The one thing I think you need to be careful of is that the bed is square when you install the wood. Taking cross measurements should ensure squareness. I used an engine hoist and ratchet straps to lift my bed off and move it around. I stood it on end to provide easy accessibility to the bottom. Of course my bed isn't in very good shape, as you can see, so I didn't have to worry about damaging it.
