There is no way to sync a PDF viewing program on a desktop with a PDF viewing program on an iPhone/iPod Touch/iPad.
If you use the wifi capacity on e.g. Goodreader and the Folders Synchronizer X by SofttoBe (OSX) you can synchronize the folders in the Goodreader sandbox. Doesn't Windows have synchronization built in? Just copy over and it asks if you want to update or replace, if I recall correctly.