1. What is Junk Folder
2. Training Spam Filter
3. Deleted folders not going away from Trash

What is "Junk" Folder

Identified Spam: Server looks at the the total score of an email and compares it with the required_score setting in cpanel SpamAssassin configuration.  If the total score is less than or equal to required_score, it will be delivered in Inbox.

If message scored higher than the required_score, server will move it to Junk folder.  If Junk folder does not exist, it will create it.

You must monitor the Junk folder to make sure no good email has been mistakenly identified as spam.  You don't need to do anything about spam messages in Junk folder.  Server will purge emails older than 10 days in Junk and Trash folders automatically.

Training Spam Filter

Unidentified Spam: Create a "Spam" folder and move unidentified spam in your Inbox. Do not move any spam messages from "Junk" folder, they were already identified by the system as spam.

Good email identified as Spam: Create a "Ham" folder and COPY mistakenly identified good email from "Junk" folder and move the original email from Junk to your Inbox or any folder you like.

Server processes Spam and Ham folders and adjust the filter every night. It will then clear emails from Ham and Spam folders. There is still no guarantee, but it will eventually help to train your spam filter.

Deleted folders not going away from Trash

This is happening because Thunderbird/Outlook is recreating the folders since it is subscribed. To fix it perform the following step.

After deleting the folder fro Thunderbird, right click on the account and click on Subscribe.  Unsubscribe the folders that were delete.