A typical lis-file name to change will be the coordinate lis-file (default name coord.lis). You can create coordinate files with different initial temperatures by using the utility program mkmaxw. Another important lis-file name you may specify is the name of the restart file (default restart.lis) to be written or read.
There is a special trick with the restart-file if you connect a '@' to the end of your restart-file name, e.g. 'restart.lis@'. In that case, EGO writes a restart-file named 'restart.lis@', but it will not use it the next time you start EGO. If you want to use that restart-file later you have to rename it to a file-name which does not end up with a '@'.