Emails not being moved from Inbox after processing & Question re Folders

Hi

I've watched the video tutorials and read the PDF Guide.

First:

After emails to an Outlook appointment, the original emails remain in the inbox, despite setting up the Options to Move Emails on all Events. What am i doing wrong?

Second:

I am confused about the Folders. I have both Desktop and Outlook folders set up that correspond to many projects. Should I use both? is there a preference for one or the other?

Thanks in advance for your reply

Tess