[General Questions and Answers] Planterz:
I'll answer what I can, as best I can.

Make sure you have BusyBox installed as well.

It's best to change

one

setting at a time. It's tedious, especially if you have to reboot after changes, but if something goes awry, it's much easier to track down the conflict or bug, especially if you're using multiple modules.

There's a definite learning curve with TB. I'm not sure why some apps might not back up. It could be because they're core components of the OS and are write protected.

When talking about batch backups, "enough" is at your discretion. No harm in doing them periodically, especially if you install a bunch of new apps. Backing up individual apps is good to do before updating them, in case you decide you preferred the older version. Or a game you don't want lose progress in or revert to an old "save".

Depends on the bloat. Some apps by AT&T or LG might seem unnecessary or unwanted, but actually are necessary and can cause crashes or force closes ("unfortunately XXXXX process has stopped"). Always back them up first, and remove them one at a time. It's better to freeze them first, then delete after testing. Personally, I don't delete bloat, just freeze it.

Both, if you want to schedule period backups rather than just doing them youself. Again, your discretion .

Batch actions and Preferences (where to store them) are all you really should be messing with now. At least until you learn more.

The logs keep track of what was granted SU access and when. Not really necessary.

PIN code is your choice. If you're the only one that ever uses your phone, it's not really necessary, but if if you let others use it frequently(for games, or to browse or log into Facebook), you might want to use a PIN so they don't simply hit "grant" whenever SuperSU requests rights. I use "prompt" as the default action, so I know what needs to access the system. For example, some apps that don't require root (like Clean Master) have additional functions if you are rooted, and this might not be clear in the description in Play. That way you know, and you won't accidentally screw something up. Also, malicious apps that have no business with root access can be identified and blocked.

You can sometimes (usually?) lose root access after an update, but it's usually possibly simply to re-root with the same method. If not, it's best to wait to do the update until others can confirm/deny. SuperSU has a "survival mode" that can try to keep root during an update, but again, it's best to wait for confirmation by others.

Read, ask, and learn. It's easy to grow confident and think you're more clever than you really are and really screw something up (I know from experience). If you look at the first couple pages of general Q&A/Help forums, you'll see lots of people who did stupid stuff and now have bootloops and crashes and bricks. Do lots of searches, here, on google, and youtube. You can often find guides for what you're wanting to do.

AdAway or other ad blocker. Not only does it block ads in your browsers, it blocks Google ads in free apps. Apart from being cleaner and more convenient, since ads don't get loaded, pages load faster and you consume less data.

BetterBatteryStats gives you much more info on what's draining your battery than the stock Android function.

Some sort of root browser/explorer is essential. You can use it to completely delete folders/data that got left behind even after an app is deleted (which can sometimes cure Google Play Store errors), among other things.

I personally like ROM Toolbox Pro. It doesn't really do anything special, just packs a ton of utilities that you can get elsewhere into a single app.

SQLite editor is necessary to do some things, but you'd better make sure you know what you're doing before doing anything with it.

WiFi Tether Router might be able to bypass AT&T's tether app. Changing some settings with SQLite might be necessary. You'd have to research this for your device.

Those are the root apps I use, as well as Xposed and assorted modules to do theming or other functionality tweaks. Xposed is quite powerful, and you should familiarize yourself with what the multitude of different modules can do. The possibilities are seemingly endless, as developers come up with no mods every day to do new things that nobody else has done yet (or ported other mods to work with other devices).

Good luck and have fun!