One of the many unique features of the Jeep Wrangler is that you can very easily remove the carpet from the floor.
PRO TIP: The first time that you remove the carpet, you will need to cut the openings in the carpet where you have to get around seat bolts and brackets. From the factory they are cut but they are not fully cut, so you will need to trim where are carpet is still attached.
When you remove the carpet you will see that there are drain plugs in the floor. There are 4 plugs, on his each foot well. If you were to flood your jeep from a water crossing or leaving the top open during a rain storm, you can pull the plugs to drain the water.
I chose that the easiest way to do a deep clean and get it as clean as possible, I pull the carpet. Over that last 2 years I have done alot of electrical work, adding and removing lights, radios, USB outlets, pieces of zip ties, wire ends and other sort of things have made its way under the carpet and under seats where I have not gotten too in the past.
The ability to remove the carpet is big advantage of a Jeep. I have done this many times with my older jeeps, it makes doing a deep clean of the carpet very easy.