Those of us just getting into the bangle.js 2

Will I have to first update the operating system and then go through and upload each app I want to use?

Yes - but this is now a very simple, easy and reliable process.
You can do it all through the main App loader at:

https://banglejs.com/apps/

The firmware updater app is at:
https://banglejs.com/apps/?q=firmware

When you get your bangle it will be installed with the firmware it left the factory with (@Gordon's garage I image). This is 2vX and you can then update to 2v13 (the official stable release) or to 2v13.x which is one of the nightly builds (or known as cutting edge). I am currently running on 2v13.13. The nightly builds of the firmware are very stable and it is rare that a cutting edge build is broken and issues get fixed quickly so I'm never too worried about updating to the latest cutting edge build.

If I have to reset to factory at any time, do I have to then go through the apps
and re-install all of them again?

Yes a factory reset set of apps is stored somewhere in the firmware and when you do a factory reset the current storage is erased and the default apps rewritten to the storage.

You can mark apps as you favourites and it literally takes 1-2 minutes to reinstall your setup. The only thing you then have to do is change your settings to your preferred defaults. EG I always disable wake on twist and set the LCD brightness to 0.5 or less.

What is best practice. I'm looking forward into getting mine.

So I would suggest something like:

1. open you brand new Bangle
   
2. update the firmware
   
3. install some apps, play around with them, install some other apps and delete others.
   
4. mark some of the apps that are not the deafult apps as favourites.
   
5. do a factory reset through the IDE, type Bangle.factoryReset() when connect through the IDE in the left hand side of the IDE.
   
6. Now go back on the app loader, select Apps and click on the More option, you should see options to 'install favourites' or 'install deafults' etc.
   
   

Repeat.