Well after taking your Jeep off-road a few times, you'll most likely find cleaning and trying to get the carpet to dry sucks. I tried to keep the carpet for a while and gave up, it just never dried out, and always smelled like mildew/creek water. I gave up and took all the carpet out, and decided to use truck bed liner on the whole thing.
There are many types of bedliner available, most of the do-it-yourself stuff is honestly pretty similar. Popular brands are Duplicolor and the Hecurliner. I personally used the Duplicolor because its what the parts store had in a gallon jug, everything else was just quarts. It took 3/4-7/8 of a gallon for me to do my tub.
Surface prep is key, if you prep the surface properly it will last, if the surface isn't prepped properly it will peel back off. I wanted to make sure I got everything so the first thing I did is remove everything, shifter boots, drain plugs, seat belts, seats, etc. Next a good washing is proabbly in order, I just used car wash soap, then rinse clean. You'll probably have to use a sponge to get all the water out, and then dry as necessary. Once the tub is clean, its time to make a mess in it again. The whole tub needs to be sanded some to give the bedliner a good surface to adhere to. I'd recommend roughly an 180 grit sandpaper, for this, maybe even a hair coarser. Your're not trying to remove the paint, just make it so its not shiney smooth. Get into all the corners and such the best you can. Once you've roughed up the tub enough, you'll need to wipe it down again. I personally used brake cleanner so it would remove any residues on the tub, and it evaporates very quickly (I use brake clean for everything). Take your time on this step, its critical to get good results.
After you got everything prepped, time to tape it off. Don't skimp on the tape, a 99 cent roll of masking tape is not what you want to use. Get a high quality roll of automotive grade, clean release tape. Sure it will cost your $5, but its worth it. The nicer automotive tape won't leave adhesive by, and gives you nice clean lines, and won't let the bedliner seep behind it. I chose to do the surfaces that the top mounts to, as well, notice the tape on the outside of the tub. There are also a couple electrical connections, best bet is to wrap some tape around them to protect them. I also left the roll bar padding so I taped it off some to make sure I couldn't bump it with a roller.
As for removing the tape. Try and pull the tape before everything dries, that way you won't chip the bedliner. I recommend pulling downwards at roughly a 45 degree angle. The sooner you can do this, the better, but make sure you get everything covered good first.
The bedliner roller kits really are handy and worth the $10 they cost. The tray and textured roller work very well. I recommend doing the surfaces that will get the most traffic first. The bottom of the back of the tub got 3-4 coats. The front floor boards got 5-6 good thick coats. Places like the sides that will likely never be touched only got 1-2 coats. Try and do this evenly as possible. Also make sure you get a cheap paint brush to use in places you can get the roller. I always first get the areas I need to with the paint brush, then go over everything else with the roller.
I was happy with the way mine turned out:
Close up of the texture:
Make sure when you decide to do this, its warm out, as it will need some time to dry. I reassembled the inside of the Jeep the next day, and left the top off for three days, as this stuff does smell. Due to the weather, I was forced to put the top back on for day four, and it did smell pretty bad in there for about a week while everything was fully curing.
At this point my bed liner is about a year old and has held up very well.