Some pictures would help a lot to understand what you are talking about.
There are rules in the NEC that require conductors to be protected in certain ways, but you are not required to run them through the framing.
Panels can be in there own room but there needs to be adequate work space required by code.
It matters not if the wiring is under the floor or in the attic in your cabin in the woods, if it is romex critters are going to chew on it.
The question of arc-fault on a water softener is dependent on it's location.