The short answer to your questions is "Yes".
For the collections, start with
https://wiki.mobileread.com/wiki/Kob...nd_Collections. That has explanation on how to setup collection management from calibre on the device.
To get the reading status from the device, use my Kobo Utilities plugin. Amongst other things, it can fetch the reading status from the device each time you connect it. It also has a function to show the annotations. Or you can use the Annotations plugin to store them in the calibre.