[trekchick]

Here's what I'd do to send only PDFs and ePubs to a folder on the HDD and automatically convert other formats using the Sony Plugin:

1. Click "Preferences", "Common Options" (under the Conversion section).
2. Under "Page Setup" (icon bar on the left) set your output profile to "Sony Reader" (I'd also reduce the margins, but that's a personal preference). Under "Look and Feel", I suggest checking "Smarten Punctuation".
3. Apply changes (green check mark).
4. If you want to preserve the cover aspect ratio, or prevent the generation of a default cover, select "Output Options", check the appropriate boxes and apply changes.
5. Scroll down to click "Plugins", "Device Interface Plugins", "Folder Device Interface". Click "Customize Plugins", and uncheck everything except PDF and ePub. Save and exit preferences.
6. Click "Connect/Share" and select or create the folder you want to use.
7. Make your ebook selections and click "Send to Device" (the device at this point is your previously selected folder). When Calibre asks if you'd like to auto convert incompatible, say yes.
8. After Calibre completes it's Herculean task, copy/move the files to the SD card using any method you like.