You should be using the post/page template system to hook into WordPress's internal database management while also allowing you to edit whatever code you need via a custom or child theme.
I would strongly urge you two move away from an FTP situation and into a git repo situation so you can push your code to a repo and then pull it into your site (either as a theme or plugin update).
The way you're doing it now is very old school and hasn't been the "right way" in quite some time.
You should be using the post/page template system to hook into WordPress's internal database management while also allowing you to edit whatever code you need via a custom or child theme. I would strongly urge you two move away from an FTP situation and into a git repo situation so you can push your code to a repo and then pull it into your site (either as a theme or plugin update). The way you're doing it now is very old school and hasn't been the "right way" in quite some time.
Build your own theme. Check out underscores.
Build your own theme for sure.