You definatly want to remove the wiring from the breaker and not leave it wirenutted. You have the basics pretty close. Make sure that you open the Main breaker for the entire house before removing the cover from the panel. And make sure you have someone to hold a flashlight for you so you can see.
There will be 2 large gauge cables that come into the panel and connect to the main breaker. These cables and and where they connect to the main breaker will still be HOT even though the breaker is open so make sure you DO NOT touch these cables. Wrap some black electrical tape around the metal shaft of your screwdriver within a 1/2" of the tip. This is so if you slip off a screw you don't short anything out while removing the wires.
You can just leave the double pole breaker in the open position and not have to remove it from the panel, this is fine. Otherwise if you want they do sell covers for panels at most electrical supply houses, and you can find them for Square D or Cuttler Hammer panels at Home Depot.
Here's a link that'll show you the steps of installing a breaker, it will cover alot of details that will pertain to you. There is a picture of a main panel inside, be sure to notice the two HOT cables comming into the panel. You may also have a ground wire you'll need to remove. Also be sure to install a knockout cover over the hole in the panel when you remove the conduit.
http://www.hammerzone.com/archives/e...er/install.htm