How does Preview manage anotations, highlighting etc

Hi,
I have been annotating a number of journal articles but when I move some of the pdf files from one location to another, the annotation/ highlighting doesn't always stay with the file. Is this information stored elsewhere on the Mac e.g. in the library? I ask because I am accessing the the files from different machines via iDisk and wonder if this is the issue. Also does Preview in Leopard and Snow Leopard deal with this information differently.

Thanks in advance.

Regards Colin