Not all formats store series information. For example mobi has no field for series. Usually this is handled using a "plugboard" to add series information to the title when it is saved to disk or to device.
Using the save to disk template or the send to device template you are in full control over how to name the book, and what subfolders to use, if any. There are some template functions to shorten fields, or you can use custom fields to set the file name.
http://manual.calibre-ebook.com/template_lang.html
You can't change how calibre name and store the books inside the calibre library, if needed calibre will automatically shorten the names and also add the unique book ID to make sure books can't have the same name and overwrite each other.