A simple tip that changed the way I work when I research a project and have to navigate multiple reference papers: merge them into a single doc.

This way I find it that it’s simpler to search through all papers, rather than switching between windows and doing it paper by paper.

To help with navigating the merged papers I usually generate a Table of Contents based on the merged files. This creates a simple click through TOC at the start of the merged doc.

Another trick to keep the merged document easy to navigate is to wrap the existing bookmarks in a parent (top level) bookmark based on the filename.

The PDF merge tool from Sejda PDF handles all of the above nicely. It comes in a web service flavour and also as a desktop application that can be installed.