I am just trying to install Fedora 18 onto physical hardware configured with a 128GB SSD and a 2TB HDD.

In the installer it gives you the option to choose the target devices. However it's "intelligent" automatic partitioner decides to put root on the 2TB volume and when I select to customise the partitioning layout it simply doesn't allow custom partitioning.

Every time I selected to install to both drives and tried to put root on the SSD it also moved /home there aswell. Now you might be thinking why doesn't he just select to install the entire OS to the SSD and then move /home later to the 2TB HDD? Well the problem you run into there is seLinux and after struggling with it's archane relabelling and recontexting utilities you are still left with annoying errors and glitchy settings.
In short the disk partitioning utility in the installer is seriously deficient.