Have you plugged the device in since you added the books to calibre and configured the collections? Assuming you have the collection management configured the same as before, this should just work. If you were using columns in the library for the collections, then they should have data and the collections created automatically.
But, there is a function in my Kobo Utilities plugin that can fetch the collections from the device into a column. That should be able to get the collections for you.
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