Cortex installs all of its instances to <cortex_root>/instances/<user_name>/<instance_name>.
<cortex_root> is c:i365 on windows and /usr/local/i365 in linux.
<user_name> and <instance_name> are translated from the username and instance name in Cortex. Everything is converted to lower case and all numeric characters are converted to underscores. So if you had a BF2 server running in Windows called clan*WTF*ranked running under user MyUser it'd be installed to:
c:i365instancesmyuserclan_wtf_ranked .
HTH