There is no fancy settings editor, so you need to change the settings with your favorite text editor. The general configuration settings are in a file named Rainmeter.ini. The skin settings are in the skin's respective .ini files.

Rainmeter.ini is in the following location:
Windows XP: C:\Documents and Settings\YourName\Application Data\Rainmeter
Windows Vista and later: C:\Users\YourName\Appdata\Roaming\Rainmeter

The file can be edited by using "Edit Settings" from the Rainmeter context menu or Manager.

The Rainmeter.ini file has several sections: [Rainmeter], [TrayMeasure], and individual sections for each config which has been loaded. The Rainmeter section contains general settings that can be used to change how Rainmeter behaves. The settings are used as default values for all new configs that are opened. Once a config is opened it will write the settings under its own section in the Rainmeter.ini file.

Important: Some of the settings in the Rainmeter.ini file cannot be changed while Rainmeter is running becase a refresh will write the old values back to the ini file. If you cannot change something, try changing the value after completely closing Rainmeter.