MAC: AE CS4 & PPro Plugin Folder

I have two questions... One is that I know that most AE filters and plugins work in PPro and visa versa. I also know that I dont have to install the same plugin in both apps plugin folder. Because one of the apps will read the other plugin in folder for any new filters. The question is which program do I need to only install the plugins at. Second Im running into a problem with Media Encoder reading some of my plugins as well and when it do that it literally stalls the encoding process. So I have to remove all plugins drag and drop them into the desktop then open and close media Encoder and restart the que. Any suggestion on how I can resolve that issue..