The Kobo Utilities plugin has an option to set the font for a book already on the device. For new books, you would need to send the book to the device, disconnect and let it process the books and then reconnect. At that point you can set the font for the books.
For collections, see
https://wiki.mobileread.com/wiki/Kobo...nd_Collections for how to set them from calibre.
To get your device library exactly the same as your calibre library, connect the device and look at the "On device" column. If there is a tick, the book is on the device. If there isn't, calibre doesn't think the book is on the device. To "fix" this, send the book to the device.