The filenaming convention you are using is fine.
You need to add your TV Folders from the preferences window, one at a time. In your case this would be the "Prison Break" folder
The program will then check that there is a tvshow.nfo within this folder.
If there is not then you will be given the opertunity to create one. The program will also download a poster and available fanarts. Season Thumbs url's are saved within the tvshow.nfo and XBMC will download them.
If an nfo exists then it is checked to see if it contains a TVDBID, this is needed to scrape the episodes. If the nfo does not contain this then again the program will scrape this information and add it to the tvshow.nfo file. The nfo file is otherwise unaltered.
Once you have added all your TV Show folders save and exit the preferences window and select the TV Show radio button, you will be able to browse the TV Shows you have added, at this point episodes can be scraped by pressing the Green "+" button located at the top. All episodes missing nfo files will be scraped along with the screenshot (if available). If you have 1000s of episodes to scrape this can take a long time, make youself a cuppa.
It has been pointed out to me many times how cumbersome the above system is, adding one show at a time and then waiting several minutes to scrape and download all the artwork before you can add another.
As a result of this I am currently reworking the whole system, this should be ready within a week or so. For more information on what is going to be changing then have a look at the progress thread in the announcements forum.
nfo files are skin independent, XBMC normally populates its library(db) from various scrapers using the internet. When nfo, tbn, fanart, and folder.jpg files exist XBMC scrapes from these rather than from the internet. Any skin that can use the library will work fine.