I'm not sure what you mean by Stencyl putting files into different drives. If you create a shared drive folder, aren't all files created there still implicitly part of "My Drive"? Otherwise, you could just create a bunch of shared drive folders and have unlimited storage, right?
You don't tell Stencyl anything about excluding folders. You need to tell Google Drive not to backup the folders I mentioned. I know that that was possible with the old "Backup and Sync" application, but that was recently removed and replaced with Google Drive for desktop which has a different set of features. If that's not possible with Google Drive, you'll need to use a different cloud storage application that does allow you to do that.