Hi Andre,
The way I understand it is that any module/addon folders in your root directory (E.g. /htdocs) will override template (.ss) and PHP code files within your themes folder.
There are really only two places you want to have template (.ss) files, within either "themes/{themeName}/templates/Layout" OR the root folder (E.g. /htdocs) inside an addon/Module folder.
Your mysite folder is used for all your PHP coding, atleast when it comes to theming.
So your "mysite/code" folder will house all your PHP files, not template files (.ss) should be sitting in here.
Addons/modules have their own folder structure, most would simply start with a "code" folder and "template" folder.
The structure would look a little like below:
-Addon/Module Folder
-code
-PHP Files
-templates
-layouts
-.SS Files
-javascript
-.js Files
-css
-css files
_config.php (For configuration)
composer.json (For composer setup)
Readme.MD (For Github)
-helenclarko