Use the Options > Load Configuration command and select a new configuration file to be loaded. This command loads either the entire configuration contents, or only a specified subset of the configuration, such as just the menu contents. See: Load Configuration.
Source Insight looks for an older version when you first install and run it. If it finds an old configuration file, it will prompt you to import the settings.
To import version 3 configuration settings at any time, select Options > Load Configuration, and navigate to your version 3 configuration file. It is usually stored here:
C:\Users\<user-name>\Documents\Source Insight\GLOBAL.CF3\
where C: is your system drive letter, and <user-name> is the account user name.