Re: Updating iPhone 5c to iOS 7.0.6 with jailbreak already.
Nobody mentioned this, so I'll add to it. If you plan to continue jailbreaking, remove all desire you have to click on software update from your phone. You'll want to avoid the OTA at all times. Most jailbreaks aren't compatible if you use this method to update your iOS. It'll generally create problems if you use it while jailbroken. You'll also want to avoid the reset buttons found in settings. These are generally a good way to mess with your phone leading to a restore.
It sounds like you're under the impression a jailbreak is the same between different iOS. That's a bit erroneous. Think of a jailbreak like a car stereo. While the stereo in your Ford Fiesta may seem to perform identical functions to that in your Chevy Cobalt, they're not identical. It's the same way with jailbreaks. They insert some code into a specific iOS that use vulnerabilities in the iOS to open up some doors. The functions seem identical, but the processes are not. That's why jailbreaks don't immediately exist with each new upgrade. Since jailbreaks are software changes, they need to be reapplied after each restore even if you stay within the same iOS. Think of it like reformatting a computer. After the format, all of your games/etc are gone. You need to install them again. Restoring your phone is simply reformatting it. Once you've done this, you need to install things again. This is why you see the apps popping up one by one as the phone syncs. Just install that one additional jailbreak app and you're set.