Make sure you run Cydia at least once prior to removing and installing Cydia via MobileTerminal. Option 12 is what you're looking for when using Terminal-based utilities like MobileTerminal or Terminal for Mac, or PuTTy for Windows. It's recommended that you not use the GUI and manually use the 'rat' command either on MobileTerminal, or any terminal/SSH based UI on a computer.
The method of getting Cydia on your device is actually the very same method. In jailbreak utilities, it's already embedded in there. Once you're rooted, and a basic SSH connection has been established, it will run apt-get install Cydia because Saurik's source was previously loaded onto your device, so it knows which directory to get it from. The source is not removed, so even after using ILEX R.A.T., as long as you run Cydia once after using ILEX R.A.T., you shouldn't run into any issues.
The method of getting Cydia on your device is actually the very same method. In jailbreak utilities, it's already embedded in there. Once you're rooted, and a basic SSH connection has been established, it will run apt-get install Cydia because Saurik's source was previously loaded onto your device, so it knows which directory to get it from. The source is not removed, so even after using ILEX R.A.T., as long as you run Cydia once after using ILEX R.A.T., you shouldn't run into any issues.