One way to help protect the inside of your jeep is with molded floor liners and seat covers.
I purchased Quadratec molded floor liners for the front, rear seats, and the cargo area. I also got a set of Seat Glovers for all my seats. So far, they are both working out great. The seat covers installed easily, but one of the straps broke when trying to pull it tight. I emailed seatglover and they FedEx'd me a bunch of new straps and plastic buckles. The covers fit "like a glove" as suggested by the name. They are neopreme and the website says they are "waterproof" but after seeing some water spilled on the seat I'm not convinced. The water doesn't bead up or pool up... it soaks in. I don't know if its making it all the way down to the actual seat underneath or not. But if you get caught in a downpour, you'll have wet seat covers to sit on. Not quite what I was hoping for.
The floor mats are great, the front pair and rear cargo area mats are nice and bowl shaped, catching all the dirt. The back seat mats are connected over the center hump, so its near impossible to take them out without spilling all the dirt they caught right back on the floor. Plus they are not a complete bowl shape, so dirt migrates out the back of the mats. However, overall I like them, they are thick and sturdy and should last a long time.