The steps for getting a book onto a Kobo device (or just about any device) with calibre is:
- Add the book to your calibre library
- Make any needed changes to the book (metadata or to the text)
- Connect the device and let calibre do it's initial connection steps
- Send the book to the device
- Disconnect the device and let it do it's thing.
Everything else you do is a optional and a complication that you decide to add. And even the second step above is not really needed. If after doing the above, the book isn't on the device and in a way you can read it, then there is something broken.
For the rest, I'm not sure what to say. Your post is disorganised enough that I'm not sure what is going on. At one point you seem to say you have shelve/collections working, but at another point they aren't. For the metadata, I can't tell if you are talking about new books or books already on the device. You need to clear up what you are doing and what you want to achieve to get a better answer.
The kepub vs epub is one that has been discussed heavily. The only answer I can give is to do whichever suits you best. The handling on the device is different, so you need to decide which way you like better and go with that.