The S4S license file, called "S4SLicense.xml", should be saved next to the Sitecore "license.xml" license file.
The default folder location is normally the "data" folder in the Sitecore website. To find the correct location for your installation search web.config for the string "sc.variable" and read the location from the dataFolder item. Note that changing the content of web.config file in any way will restart the website.
If you are replacing an existing license file, the old license content may be cached. To clear the cache it may be necessary to restart the website (or wait until the cache expires).
See the example license file attachment.