I personally recommend moving away from PDF as a reading format. However, that's kind of hard to do for some reason authors keep sharing their fics as PDF.
I've yet to see a PDF that looked good on a 6 inch screen and no author in my two years of expererince has ever offered a PDF actually created with a 6 inch screen in mind. As a result when you add regular 8x11 PDFs to the Sony you end up with wide margins and tiny text.
I have no clue how the Kindle will convert the PDFs but I've heard mixed reviews.