Running a high amp line into the cab is never a good idea. The only wires that go into the cab should be behind a relay/switch setup,or at least a fuse/breaker of some sort,(battery cables shouldnt have anything). If you have a short in the line, its up against carpet which is quite flamable and directly under you.
In saying that its one of those things that will probally never be a problem so you can argue both ways forever. (I do safety consultation in the mining industry on the side so pardon my paranoia)
Unless you have an ultra low ride that scrapes on gumnuts then using split-loom to cover your cables will provide more than ample protection. When running cales, always have plenty of extra since by the time you go up and down and around, you tend to use much more than you think.
I would suggest that you run the cable under the body and into the tray. Use black split loom to protect the cable, plenty of cable ties to pull it up to the chassis, and when you pass through metal (ie the tray) use gromets and silicon to protect it. My cables in the pootrol are all 19mm diameter.
As for earths, the more the merrier, and size is not as critical as the active cable. In my Pootrol I have earth leads on both batteries
from battery to body
body to engine
body to chassis
engine to chassis
fuel tank to chassis
These are all about 10mm diameter in size.
As for cable size, in order to correctly calculate the actual size needed, a good online calculater avaiable here is a good rule of thumb. I sat down with a sparky, and confirmed the results that the web page gave, so its pretty accurate. Assume an acceptable voltage loss of 5% max, 3% is better, but probally excessive.
A quick calc of 5% drop, 100amp draw, 5m cable run and 12V system yeilds a 50mm2 cable.
online cable size calculatorDC cable calculator