In the olde days of the DF, I always carried the back attached to the camera as the DF body in a protects the back with the eyepiece on top and the rest of the camera body is brick so it's very hard to damage the back unless you drop the rig.
When I moved to the Arca, at first I was a bit concerned as for some reason on the Acra pancake body the back just seems to stick out with nothing to protect it from the sides. So I carried the back in a padded case with the Phase One cover. After a while I got very familiar with how the Arca holds the back to the camera and I was no longer worried about it so I just carry it attached to the camera. I use either a F-stop bag, with the large PDU or I have the waterproof bag/insert from the LowePro waterproof setup which I carry inside a Dana Designs backback (when I am going to be crossing a lot of streams). In either solution, I place the back LCD down with the tech camera towards to outside of the pack The Acra rm3di takes a lens cap that fits inside the opening of the lens mount and that protects the sensor. If I am carrying my 35mm Schneider I will leave it in the camera since this lens is so short. Most of the other lenses are a bit tall and tend to protrude past the depth of the pack. I also am a bit wary to carry the 40mm Rod mounted on the camera since the 40mm and 32mm have a lot of lens weight in front of the shutter and can get damaged due to a fall (by me which will happen at times). I like to keep the lenses in separate plastic containers with padding.
The Phase One backs are well made and durable. However as I recently discovered, the IQ2's have a bit of a issue with the cover for the wifi. This cover is plastic thus this part of the back is not really protected as well as with the older IQ1x backs. Mine is currently back in Denmark having the cover replaced since mine has come loose. It seems the first round of backs had a different way of fastening/gluing the top piece to the frame. My point being that in the future I am going to be a bit more aware of how the back is placed in the pack in relation to the wifi cover i.e. making sure nothing is pressing on it.
Paul Caldwell