You can create them at any time, including during the installation of Zorin OS. Since you mention that you are going to wipe the drive entirely, I assume you already have your data backed up elsewhere?
If so, you can follow the instructions from this post to install Zorin OS with a dedicated partition for your user files:
How much space to allocate to each partition is up to you, as it depends on how many files you have, software you install, etc. For a 500 GB drive you can allocate about 200 GB for the system and the rest for the home partition (steps 5 and 6, respectively). That should give you a good balance to get started at least.
And no, you don't need to worry about what Flatpaks are. It's just particular way of packaging software that has a few caveats here and there, sometimes useful but sometimes annoying to work around.