PeakHour 3 is a brand new app and because of the way Apple (and in particular Mac Appstore) apps are sandboxed, it's not possible to automatically migrate settings across.
If you would like to manually copy your settings over from PeakHour 2, follow these steps:
Depending on the distribution of PeakHour 3 you have, type the following commands:
cp -r ~/Library/Containers/com.digitician.examinet/* ~/Library/Containers/com.digitician.peakhour
cp -r ~/Library/Containers/com.digitician.examinet/Data/Library/Application\ Support/PeakHour ~/Library/Application\ Support cp -r ~/Library/Containers/com.digitician.examinet/Data/Library/Preferences/com.digitician.examinet.plist ~/Library/Preferences/com.digitician.peakhour.plist