Hello,
AN4769 describes how to implant a single Processor Expert driver (or the source code of it) into a non-PE IAR project. This application note does not replace the 'Add project connection' feature of the IAR workbench. That connection is for a 'live' connection between Processor Expert/Eclipse and IAR, so you can go to Eclipse, generate code, and then it the IAR EW will know about the changes and update the IAR project accordingly.
As for your case (as I understand it), I would suggest that you use the 'add project connection' and generate the drivers in Processor Expert. Once this is done and you do not need Processor Expert any more, you can use that project without Processor Expert, just using in IAR the created source code.
Erich
PS: in case you consider using IAR in Eclipse: Tutorial: Replacing IAR EW with Eclipse IDE | MCU on Eclipse