I have had to manually go into each and every series folder and delete the extra files/folders. Be sure to use ORGANIZE first. A scan of the disk will only put the items in the DB as found, it will not move them into the right season folder, only organize will do that. Well when the file is downloaded it will put it in the correct folder but that is normal.
What I have been doing to convert over Sickbeard is to move the series over to a new folder I set up in Sonarr as the series folders. I have found that if you have folders that are say show S01, S02, ect, rename S01 to be without the S01 so it is just the series name, then move the S02 ect over to the renamed folder. Then move the renamed folder to the Sonarr series directory. I do this for 10 to 20 series. Then I go into Sonarr GUI and do an add new series via bulk disk scan. Tell it the directory to scan, and the new series should pop up. Add them to the Sonarr. Once you have added all the series, do a disk scan from the add series menu. Sonarr will find the new series shows.
Here is where it gets difficult, once Sonarr is done scanning new episodes, go into each series and do an organize for each. After done organizing, you can go into each folder and delete the extra files/folders that are in the series folder.