First you should create the custom template which is explained really well here:
https://www.zen-cart.com/tutorials/index.php?article=142
The override article here is also very helpful:
https://www.zen-cart.com/tutorials/index.php?article=143
If you follow these articles, you will already have the custom folders you need without having to create them as you need them. Except for the main folders, I have been creating them as I go (bad beo, bad, bad).
I normally create the custom folder in the area I need (if I haven't already done so), copy and paste the page I will be working on (like flat.php) into the new "custom" folder, open that page, and then make the changes. Then I upload to the server.
Of course you don't have to call your template "custom". You could call it "mint_julep", but I find "custom" works well for me.
The main thing I have found with the custom template is to take my time and follow the steps one by one. So far I haven't had any problems.
Good Luck and God Speed!
Beo
:clap: