Quick tips

Check "View > Hide read feeds" and you have much less clutter in Feedreader
Check "View > Hide read articles" and Feedreader will open feeds faster. You do not have to delete read articles. They will be deleted automatically based on archive size of feed.
You can change update frequency and archive size of all your subscribed feeds if you go to "File > Feed management" and press Control+A or select multiple feeds from left pane.
To trigger update of selected feed double click on feed icon on the left hand panel.
If you would like to see bigger notification window then you can just resize it. Also it's possible to move notification window to wherever you want it to be in desktop
If feed only contains link to article then you can make Feedreader automatically open this article link by checking "Open article link automatically" in feed properties