MAIL & SALESINBOX: Email messages that have been read and processed remain in the Inboxes?

MAIL & SALESINBOX: Email messages that have been read and processed remain in the Inboxes?

Both in MAIL & SALESINBOX, I noticed that email messages that I've opened, read and processed etc. still stay in the inbox.  
What are best practices when, where and how to auto-move them depending on their state?

Uwe.