If you want to keep all settings of a previous version (like customized excluded registry entries, excluded drives, paths to search for matches), then you should install each new version over old version without uninstalling into the same folder.
If you never made any changes to the configuration in Registry First Aid, then it does not matter how you install a new version unless you are registered user.
If you are registered user and do not want to enter your registration key (serial number) again then you should install the new program version over the existing one and into the same folder.