Vienna comes with some great help, just pull down the "Help" menu (when Vienna is the front-most program, and the Help window will open up. It explains quite a few things, but (currently) doesn't go much detail with regard to the Preferences. Mainly this is because they are kind of obvious and self-explanatory, but just in case you are not sure... read on...
Here are two views of the Preferences window. On the left is how the Preferences window looks the first time you open Vienna, these are the default preferences. You can see there are three categories of preferences: General, Appearance, and Advanced. Let's take a look at the General preferences first.
On the left are the defaults, on the right is how I've set them to my liking, and below, I will explain why.

First, I customized where files that are downloaded go to. I don't like downloaded files going to my Desktop, too much clutter. I send all my downloads to a "Downloads" folder. And within that main Downloads folder, I have some sub-folders, so later, I know which program was used to download the files. However this is my logic, and I rarely use Vienna to download files. But it may be that you use Vienna to download podcast files, or some other types that are better suited to go to other folders. In that case set it up to your liking. If all this is "Greek" to you, then rest assured you can come back and customize this later.
Second, I checked "Open new links in the background" and "Open links in external browser." I prefer to read the news items in the web browser of my choice, thus I checked the second option. And since I like to stay in Vienna, and choose which of the many news items I want to read more information about, I checked the first option "Open new links in the background." This causes Vienna to stay the front-most application, and it sends a message to the default web browser to open any links I tell it to.
If I didn't check "Open new links in the background," each time I clicked a link, my web browser would come to the front. And personally I like to have the web browser stay in the background, opening a new tab for each article I wish to read.
My next preference is to set Vienna to "Do nothing" when new articles are retrieved. Having the icon bounce in the OS X Dock is annoying to me, and I have so many unread articles I don't really need to see how many unread articles I have.
Finally, I set Vienna to call the article read after I move to the next article. However, you may prefer the other option, to mark the item read after a short delay. You can keep this Preferences window open, and beside the main window, and try both. Figure out which suits your style better.
In the Appearance category of the Preferences window you can set the various font options. Depending on the size of your monitor, how good your eye-sight is, and other stuff, you should customize this to your liking. Note the helpful "Never use font sizes smaller than X" option. This is good because some web sites set the font size to be much too small. I also suggest making sure to check "Show folder images in the folder list." This will cause the web site's "favicon" to be show in the Folder list, making it easier to quickly find the news feed for a particular site.
Finally, as a security precaution, I turn off "Enable JavaScript in internal browser" in the Advanced category of the Preferences window. Even though I don't use Vienna's built-in web browser, I turn this off. You can read more about this in the online Help that comes with Vienna.
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