Basically all Sony PRS-Reader use the Sony Reader Library (download from Sony or from the CD) to manages your e-Books and download them to your reader.
But you may try calibre (latest version 0.7.19,
download here) which has a lot more features and supports PRS-350 too. calibre manages your e-books, convert them between many formats (pdf, epub, mobi, etc.), download news from the web and send all those to your reader. calibre supports a lot readers (sony, kindles, nook, etc.).
calibre has it's own forum at MR.