Change Preferences -> Sending books to device -> Save template or (probably better) override this default in Preferences -> Advanced -> Plugins -> Device interface plugins -> Kindle 2/3/4/Touch Interface -> Customize plugin -> Save template. Remove anything up to and including the last / and change the rest to whatever you want.
What I use on my Kindle Fire (no folders allowed) is:
Code:
{author_sort} - {series}{series_index:0>2s| - | - }{title}
Note that if you have many ebooks (certainly thousands and perhaps hundreds) your Kindle 3 will slow down for file operations if all the ebooks are in one directory. What I use on my Kindle 3 is:
Code:
{tags}/{author_sort[0]}/{author_sort} - {series} {series_index:0>2|| -} {title}
You could remove the "{tags}/" and still get 26 sub-folders from the "{author_sort[0]}/" and this is likely enough to avoid a filesystem slowdown.