This is what works on my PRS-505...
- Highlight one (or more) of your PDFs in the Calibre Library window.
- Edit Metadata from the menu. Move down to the Tags box and type Periodical (or Journal or Article or ... whatever you want your Collection to be called on the Sony) and press OK. Your new Tag name will be visible in the Library Tags column.
- This is a once-only operation. Preferences - Plugins - Device interface plugins - select Sony device - Customize plugin button. Then in the bottom box make sure tags is listed. It may already be as the default is series, tags.
- Connect your Sony to calibre. Let it do its stuff. If your PDFs are already on the Sony then disconnect, otherwise send-to-device your newly-tagged PDFs then disconnect.
- Go to Collections on the Sony menu and you should have a new one called Periodicals (or whatever) which lists all those books with the new tag.
- If, by any chance, this doesn't work for PDFs already on the Sony then just resend them. (Can't double-check at the moment as my Other Half has just waltzed off with the PRS505)
Caveat: If "Periodicals" has a special meaning on the new-model Sonys, like your PRS650, perhaps you should pick a different name for the new tag.