You can set the licenseFilePath for each site in the EPiServerFramework.config. See:
That solved my problem. But the licenseFilePath attribute should be set on the site node i EPiServer.config.
Doh, you are right Johan - glad I solved your problem anyway :)
We have ordered one Additional License which is bound to an ip and then an 2nd Additional License, 3rd Additional License and 6 4th Additional License. 9 in total.
How do we install them to the sites? We only have on web root. Activating them from EPi Admin doesen't work, it just says "Failed to call GetLicense. Reason License does not exist for guid" or "Failed to call GetLicense. Input parameter cannot be null. Parameter name: String".
If we download them from the licensing system we get multiple config-files.