In order to help you better, we really need to know what year and model of Jeep you have. I suggest you put that information in your sig, that way you won't have to remember to put it in every time you post. It is also a good place to list current and future mods. This helps let folks know what direction you are trying to go with your particular Jeep.
Pretty much the best way to clean your tank is to drain it, then take it off the vehicle, remove the fuel pump and using lots of rags, reach through the hole where the fuel pump goes and wipe the bottom of the tank down. You're going to have to get pretty inventive if you want to reach most of the bottom, though, like taping a ball of rags to a copper tube for example.