I suggest looking at the
Reading List plugin. With it you can create lists that send books to the device when connected, or update themselves to show the books on the device. Or any other purpose you want.
Marking books as read is a frequently discussed topic here. There are a lot methods: a Reading List, a yes/no column, date when read, adding a tag. Of course, as you have a Kobo ereader, I would recommend my
Kobo Utilities plugin. It can pull the reading status from the device when it is connected. Along with a lot of other things.