The 'special link' is the mount command which attaches a partition to the mount point, ie a directory in the root file system (or any file system already mounted). So the installation program will take care of that.
But don't put /etc on a separate partition. Apart from the root fs, all file systems are mounted by the rc.sysinit script which is started from /etc/inittab. The script itself is in /etc/rc.d. So the /etc directory must already be present for this to work. Other directories that should be on the root fs are /bin, /sbin and /dev.
At least that's the way it works on Redhat. I've no experience with Slack, but I assume there's a similar configuration.