To use it you'll have to create a bookmarks text file that looks at a bare minimum like this (bookmark title/page number):
Then all you have to do is:
1. Open the .pdf file with JPdfBookmarks.
2. Click the Load Bookmarks from a text file...
button and select your bookmarks text file.
3. Save the .pdf file.
For more information, see the program's Wiki page
The only downside is that JPdfBookmarks is a bit slow. If you have an older machine or a very large .pdf file, it might take some time until all bookmarks are added.