Running wire routes from electrical panel for crawl space cabin?

Purchased 650 sq' ft. cabin in Northern Michigan. It's foundation consists of fottings and posts offering a 2' distance between the bottom of the joists and the ground. Can crawl under there.
The wiring is all 50 years old and I wish to completely rewire the entire cottage. There is a 100 amp QO Square D panel installed on the outside of the cabin in a homemade wetherproof box. I wish to flip the panel to the inside (actually switch to a 200-amp QU panel), and need to know the following: 1) Should/Can I run the 15,20 and 30 amp lines DOWN underneath the cottage thru the center of the joists then up through the mud/bottom plates, and if so, can i build a "closet" for the new panel in the bedroom, and run the lines straight down through the floor, do they need to be protected (armored cable, conduit either metal or plastic), or through a mud/bottom plate? Or would it be better to run the lines UP through the ceiling (and can they go right thru the drywall in this electrical panel closet or do they need to be through a board of some sort, and then run them through the center of the ceiling joists?
Wondering if an underneath route could ve vulnerable to animals chewing, and would they have to be in conduit or underground cable? Is the route of choice through the attic?
Can there be a closet door to the electrical panel closet, and does the panel have to be attached to a wood board on the wall?
Also are Water Softeners supposed to be on a AFCI circuit? Thank you alot!

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.

The panel in a closet can be a problem. There are specific "clearances and free access" requirements, that often cannot be met in a smaller closet.