I have various small bags tucked into empty spaces that I found. A wrench roll and pipe for lug wrench extension fit in with the jack. My extended cab truck has fold up seats so between the hinges on each seat is a pair of small bags that have my bob and other gear. Under the seat where accessable from a driving position is a small first aid kit. Each smaller bag has an main purpose and then has a couple secondary items that are redundant with the main purpose of another bag to help in the event of damage/loss/theft of another bag/kit.
There are trunk organizer system and various cargo nets you can buy as well as bungee cords and such or you could try bolting in some tie downs like what are found in trucks/vans though I've tried all those and none worked well. I'll go against the current anti-suv trend and say that a truck/suv is the only thing I will ever own, I gave up on trying to make cars work even half as well at doing anything more that just simple people hauling.