Unfortunately, in the current version it is not possible to use paths that are relative to the emulator's installation directory in the configuration files. They can only be relative to the current directory, which, on Windows, might be where the ep128emu.exe is found at startup, but I am not sure if this is always the case.
If the configuration files are generated automatically with a program, then it is possible to find out where the emulator is installed from the HKEY_CURRENT_USER\Software\ep128emu2\InstallDirectory registry key.