Hi bll0,
For all snippets that are added from within the Manager, the code is stored in the database - the good news is that you can run off external files easily.
For information on how to set up snippets to run from the external files, xwisdom published a great tip in
this post.
In terms of directory structure, for snippets/modules/plugins that require external php files, the directory structure is as follows:
/root of website
|
|_/assets
|
|_/snippets
|
|_/mysnippet
|
|_/modules
|
|_/mymodule
|
|_/plugins
|
|_/myplugin
Under each of your custom folders, you could break the directory structure down even further if you wanted but that is really down to personal preference. For example, you could have folders based on the type of file: css/js/includes/images etc.
Hope that helps, Garry