How do I set up MailScanner to store a copy of all emails in quarantine?

You should ensure you are running an up to date version of MailScanner and the front-end.

Go into WHM > Plugins > ConfigServer MailScanner FE > Click the "MailScanner Performance" button > Click "Enable Store Messages".

From that point on any messages coming in will have a copy stored in quarantine and will have additional options at the bottom for Release (not available if it contained a virus or other infection, but will be available for non-infected blocked attachments), Delete, and SA Learn. The emails will still be delivered to the recipient (unless they are blocked or deleted for some other reason), but a copy will be stored in quarantine for 7 days by default. To change the number of days emails are stored in quarantine, go to WHM > Plugins > ConfigServer MailScanner FE > MailControl, click the Menu button (top right), select MailControl Settings, and change the value for Keep x days of Quarantine entries.