I've never been able to get this to work so must be doing something wrong. I'm trying to read this PDF(The link is at the bottom of the page) and be able to add notes on my iPad say, but then be able to read it on my iPhone and see the notes/add more notes to it. Problems I often have are having to make a copy of it on each device as it can't be saved or it's in my iBooks on one device but not another (eg - I have a Pro Git book in my phone, but it's never made it to my iPad). I've tried a coupe of different apps and read links also, so I must be missing something fundamental.
As suggested by the OP, from the comments:
Depending on the PDF viewer, the PDFs could be stored in the cloud, using something like Dropbox. Synching is supposed to work in this environment.
If it is just for commenting, decent PDF viewers are Adobe Reader or iOS, or (in any case) PDFExpert by Readdle.