As would be expected for a 20 year old rig, the floor of my TJ was looking pretty beat up. It hasn't had carpet on the floor in the back since I bought it, and getting rid of the carpet on the floor up front has been on my to-do list for a year. Carpet deadens road noise and it often has a heat barrier as well, however it traps water and mud, leading to rusting.
Truck Bed Liner is a common choice for coating the interior of Jeeps and similar rigs due to it's durability, but a bit of extra work can make it an even better choice.
First thing you should do when coating the interior of your rig is pull all the seats, center console, drain plugs, and anything else that prevents putting down a thorough even coat. Then clean it all thoroughly, "scuff" sand it, and clean it again with degreaser.
Here's where I add the extra step - I mix ceramic heat insulating powder 50/50 with flat black tremclad and use it as a base coat. There's a lot of mixed reviews out there on insulating paints, but this is the third vehicle I have used this particular method on and I have found a noticeable reduction in heat. Between when I brushed on the base coat and when I rolled on the liner I drove 45 minutes in slow highway traffic. Normally the side of the transmission tunnel would get too hot to hold my hand against it. With the coating it was hot, but still tolerable.
Once the base coat is completely dry I lay down the bed liner, starting with a brush on the edges and corners, and then rolling it onto the flat areas. I go right up to the edge of the tub and coat all the sheetmetal from the firewall back to and including the tailgate. After the roller work I quickly go back with the brush and spread out any Liner that is puddling or dripping. You can use a sprayer rather than brush and roller, but then you need to spend a lot of time masking off anything you don't want to coat, and bed liner is notoriously tricky to spray.
After the liner dried I upped the heat blocking even further by coating the transmission tunnel with insulating foam. If you do this make sure to use a sealed-cell foam or other water-proof insulator. I then cut the carpet so it just covers the transmission tunnel and the rear fenders and reinstalled it. Enough carpet to make the interior more more classy and comfortable but nothing on the floors to hold water.