I worked it out. Its simple.
1. USe a plugin to access the driver. He the Extended Kobo Plugin
2. State you want to have collections, and use the "tags" column
3. ensure Automatic metadata is also checked
4. Then, click on preferences/metadata and remove or map tags you dont like. Also limit the # of tags per book
5. Clean up your current calibre tags (manually, search/replace, or delete, re-download)
6. Now when you connect your Kobo it will sync.
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