I’ve set up sonaar using the scan existing library function - and it detects everything correctly; however, when it parses the files after download, instead of placing the files into specific series folders, it places them into episode folders in the root directory (ie, directory contains folders such as ‘seriesxxx’,‘seriesxxxS01E01’,‘seriesxxxS01E02’, after a new file is processed by Sonaar). Can anybody indicate to me what might be a simple solution to this?
Sonarr doesn’t put things in episode folders (and only sorts under the series folder). It sounds like you have unsorted (files downloaded by your download client) and sorted files (those sorted by or before using Sonarr). You need to separate them and Sonarr will sort them, just make sure Completed Download Handling is enabled.
Something other than Sonarr is sorting them (your download client likely), you will need to fix your configuration and not mix sorted and unsorted files then look in the log files for errors with importing.