After your media files have been converted to the proper formats, you need to copy them to the web server folders if they aren't already there. If you are using aliases, then they are probably already where they need to be. If not, copy them to the folder structure under your web server root folder.
The video files can be copied directly into the Videos folder, or they can be put in subfolders under the Videos folder if you want them to be a little more organized.
The music files should be organized under the Music folder by Artist\Album\Songs. Folder and song names with punctuation such as spaces, apostraphes, dashes, underscores, ampersands, and parenthesis are allowed. However, don't use slashes or double quotes in the folder or song names. Here is an example of how it might look:
This shows the Artist and Albums folders. The songs would be in each of the Album folders with the mp3 or wma extension.
The photo files should be organized under the Photos folder in subfolders, usually by the date they were taken, however, you can group them into folders however you want. The groupings don't need to be consistant either. Some could be by date, others could be by activity, event, or any other type of grouping. Here is an example: