I use a duffle bag (mastercraft walker evans bag). It holds most of the smaller spare parts and all of my tools, bottle jack. The only things not in the bag are the larger spare parts that are strapped to the tub.
but in a rollover the duffle bag itself becomes a hazard, so I strap that down too.
inside of the duffle bag I have smaller tool bags to keep them organized.
I only put the duffle bag in the jeep when I take it out to go four wheeling, which is only a few times a year lately