The first question: click on the preferences tab in the upper right corner of your iNotes mail file, and change the Check for new mail every X minutes line....
The second and third are explained here:
http://www.redbooks.ibm.com/redbooks/SG246518.html
For the database bookmarks, you can think of creating a custom page or frame and using html anchors to the databases, or use the standard features in the welcome page.
There are e few differnces between R5 and R6 but the you should be able to find your answers here.