To be able to open GoToR hyperlinks within the same WebViewer instance, you would have to take the following steps:
1) Pre-processing: Iterate over bookmarks in a PDF and add a special labels to GoToR bookmarks
Note: that relative path might not work, since it will be relative to your server root not the PDF. So during the steps 1 or 2 you might want to expand it to correct relative or absolute path.
Let me know if you have further questions. If you let us know more details on the problem are you trying to solve, we might be able to recommend a better approach.