Welcome to the world of phone freedom - it's a whole new world once you're out from under the thumb of Big Red...!
Your questions are all excellent and I'll give you my $0.03 (inflation, you know...):
1) TiBu requires USB debugging be enabled for proper functioning. I don't know why. But if you've not got it enabled, TiBu will throw up a splash screen warning you that it's not gonna be able to do what you want it to do.
2) No reason to keep unknown sources checked. A nice new process in one of the updates (don't know whether it's a Sammy thing or a 4.x.x thing) is that it will go back to unchecked when you side load (it'll flash a warning about unknown sources in setting when you try to side load and you've not checked ok to unknown sources. When you go to settings to allow the install, it'll have as default to go back to secure, not accept from unknown sources after this initial install - works very well). So just keep it off and you'll only check it when you need to. While it's not an issue just yet, this makes sure no one can install some malware without your doing the dumb thing and saying yes to it.
3) Use TiBu to make a schedule or two. I have it renew all my backups twice weekly. It's not something you HAVE to do, but if you want to wipe and flash, you've got access to you most recent apps and settings. Be sure to be careful with TiBu though - it's powerful and with that power, you can f*** your phone up pretty badly. I recently had a schedule to wipe cache 3x/week and it ended up killing my alarms... Try to explain to your boss your late because you're a geek...
4) Root is pretty secure. You can lose it in an update but assuming you've loaded MJE 4.3 and you're happy with that, you'll never lose root unless you purposely rescind it. You'll likely not if/when you update to 4.4 either but I've heard tales of people changing ROMs or updating and losing root. It's never happened to me but stranger things have, so I guess it's possible.
Welcome to the cutting edge! It's freaking awesome up here!
You just changed your smart phone to an effing genius phone! Congrats!
"I've got a revolution behind my eyes..."
"You Live & You Learn - Or you don't live long..." --LL