Modify downloaded theme

[Meinerwold]

When I export my theme is there a way to copy and paste product codes, css files, basically the whole content, when I export I just get the six folders. Templates, assets, snippets... Where can I just and past my modifications to, like the index file, product files, and such

[Meinerwold]

Also how do I get it all back together so all files are in the correct folder