I am still confused. No matter what program you are using to run your PDF files, you have to open it in a different window. For me, the Acrobat reader is only for use when I only want to view PDF files and don't want to edit them or do anything fancy with them. For instance, I have the free Acrobat reader on my server so I can read directions for installs and stuff.
So, fine your favorite PDF application (there are tens and tens of them), uninstall everything else so there are no conflicts, and then edit away. Once they are imported, you can left click to see them in the viewing pane on the right and right click and choose open in native application. I think the options that Jon gives you such as Delete, Open, Sign off, Edit and Print is rather good.
