The Addon Manager doesn't change or do anything to your affinity mask. It READS the existing value from your existing Prepar3D.CFG file, and it just offer you an easier interface to set it, instead of trying to figure out binary arithmetic.
It's only after you press the SAVE button, than any settings will be changed.
If you didn't had ANY affinity settings, the program will display a default value based on a good setting for a quad-core system, but again, nothing has changed yet, you are only looking at the value that WILL be saved to your .CFG file IN CASE you'll press "SAVE" button.
As far usage is concerned, the top row of CPUs are the "real" cores, the 2nd row are the "logical" cores from hyperthreading. This means, depending if hyperthreading is enabled or not in your system, you might want to enable the logical cores or not.
A good practice is to leave the 1st physical core to Windows, and all the rest to the sim. Which translates into:
- All the top CPU icons enabled EXCEPT the 1st, if hyperthreading is disabled in the BIOS
- All the top AND bottom CPU icons enabled EXCEPT the 1st on top and the 1st below it, if hyperthreading is enable in the BIOS
Of course, if your system is a quad-core, you'll will have to enable only 3 cores, if it's a six-core only 5 cores, and if it's an 8 cores, only 7 cores (to leave the 1st to Windows).