If you have not upgraded your Mac to OS X 10.10 (Yosemite), then iCloud on your iOS 8 device won't be able to talk to your Mac running OS X 10.9 (Mavericks).
By switching to iCloud Drive in iOS 8 you are switching over from the old iCloud. Your files get copied over onto iCloud Drive right at that point, and are no longer linked to any file in old iCloud, which is where the file on your Mac are linked. Only iOS 8 and OS X 10.10 (Yosemite) devices can now sync files. There was an article in Macworld that has more detail.
We recommend syncing files to PDFpen on your Mac with Dropbox. In PDFpen for iOS you can add a Dropbox sync folder.
(Applies to PDFpen in iOS 8 and PDFpen in OS X 10.9 (Mavericks)).