Hello
You can protect a folder and have no association at all. Simply the folder is protected, when you unlock it the data is accessible when you lock it, the data is protected.
The application association is referring to the Espionage 2 functionality which was so far missing from version 3, it is kind of an automation, when you unlock a folder then it will trigger the application to launch, say, whenever you unlock a folder containing your tax spreadsheets, this means you want to work on them, and for example Excel will be needed, so to save you one click, when you unlock the folder, this will also launch Excel for you.
You cannot protect single email, you can either protect all your email data or nothing, as Espionage protection is folder based, so it will protect the folder in which all your emails reside.
let me know if it is still unclear.
Rgds
Zsolt