A properly formatted .reg file for PES 2010 only touches keys under KONAMI\PES2010 . It cannot harm your OS. Malicious .reg files, however, can delete or alter system keys. Always inspect the file in Notepad before merging.
A dedicated (with a .reg extension) automatically creates these exact keys in the right location (the WOW6432Node path) so your 64-bit system recognizes the game as properly installed.