If you want to upload one or more .scm/.scx files, then choose the top file picker. If you want to upload entire directories and their sub directories, then choose the bottom file picker.
Also, please don't worry about corrupt, broken, unfinished, testing, rigged, unprotected, duplicate or outdated maps. The website will handle all of this and many of them are important parts of StarCraft map making history. Even uploading the exact same archive multiple times is no concern. So, please upload everything you have and let the site do the filtering and processing. Try uploading your entire StarCraft map directory: <USER_HOME>\My Documents\StarCraft