Is there any tool in some PDF Viewer/Editor like Acrobat, Evince, etc. where I can navigate and watch coordinates(i.e. (x,y)) of any selected point in PDF-document?
In case you don't want to install any heavy software for such a trivial task, you can create annotations in a xfdf file, set their location and then see which area is annotated in PDF.
You can use this template:
Change the coordinates of the "rect" attribute, save the file as xfdf. Then, as you open the xfdf file in Adobe reader, the reader will ask for the location of the PDF file. Locate the PDF document, and you will see the rectangle drawn at the specified coordinates.