Hi all, I'm the developer for the save system and I'm happy to answer any questions you have. I'll try to answer everything which has been asked here, but let me know if I missed anything.
Firstly I'd like to mention that Google Drive behaves differently to Dropbox and OneDrive. All 3 services feature a "application mode" which gives an application access to a special folder on a users cloud storage specific to that application, instead of general storage. For user piece of mind this is obviously preferable. However, we decided that users should always be able to access their projects outside of the C3 editor, and unfortunately Google Drive does not allow this in when in "application mode". So we only use it for Dropbox and OneDrive.
We are planning to implement folders, and some work has been done towards this for Google Drive. But it's still some way away. At the moment any file with a capx or c3p extension in your Google Drive will be visible in the Cloud Dialog regardless of if it's in a subfolder. So can in fact move the files into a subfolder using the Google Drive website, and when you attempt to save to it next it will stay in that subfolder. Any new project will be created at the root of the project.
It's also worth noting that I'm currently hunting down a bug where either some or all files don't appear in the dialog when first shown. I'm not 100% sure what's causing this but I think it might be a problem on google's part. It can generally be fixed by clicking the refresh button at the top of the editor. It also stops once your Google Account session has "warmed up" for some reason, I only see it immediately after selecting an account ( this session lasts for an hour ).
Finally matriax the Browser Local saves exist in a special database on your hard drive controlled by the browser, and they do not appear as files on your computer. It's not possible to get access to the normal filesystem via the browser ( for user security ). However, in the future we will be releasing a desktop variant of the editor that can access the normal filesystem so you can save locally.