What exactly do you need to know it's pretty simple.
APP Settings can be saved With Titanium backup. But the point behind a factory reset is to start from scratch. It does no good it you put the same crap back on your phone.
A factory reset can be done a number of ways
TWRP
CWM
Stock Recovery
Settings menu
All of them do the exact same thing. It deletes all of your apps, settings, passwords, accounts. It makes your phone the same as if you went to a store and bought a new phone.
It Deletes everything except what is on your internal and external sd cards which it doesn't touch.
Some apps such as nova can save there settings. Nova has a save setting option and the settings will be saved in mnt/sdcard/data/com.teslacoilsw.launcher/backup folder.
Your best friend as far as restoring apps is Titanium Backup. (Get the paid version this is too important to be cheap.) If you can't afford this you shouldn't have bought this phone.
Titanium backup saves all of your apps and app data to your internal sdcard by default. It does this because it knows that files saved here are safe from factory reset. Unless you go in and purposely format your internal sd card or external sd card data saved here is safe from most wipes and formats.
If you have any specific questions ask. This is pretty basic stuff.