I do not know if you're using Windows or Linux, but I have configured steamcmd to install KF to several folders, such as:
~/kf-server-1/
~/kf-server-2/
~/kf-server-3/
etc.
Then, in side every /kf-server-x/System I've edited KillingFloor.ini. I assume you're familiar with port forwarding and port configuration in KillingFloor.ini (if not, google "KF Dedicated server wiki").
I've edited the ports so that kf-server-1 operates on port 7707, kf-server-2 operates on port 7807, kf-server-3 operates on port 7907 and so forth. Works without problems.