The easiest way would be to duplicate your dedicated server folder and change the server name, game (and insim) ports. alternatively duplicate setup.cfg (but change the same variables) and add /cfg=name_of_new_cfg.cfg to the command line.
example:
copy setup.cfg -> setup2.cfg
edit/create server2.bat like so:
LFS.exe /cfg=setup2.cfg
It is vital that the servers are run on different ports and have different names.