Installing tools into different directories is not supported in ISE Design Suite 11 or later. You must now install all the tools into the same directory. For example, the default installation location on Windows is C:\Xilinx\11.1, a supported setup would look like this:
It is possible to install in a different location as long as everything is installed in that same location, that is the ISE, EDK, PlanAhead, and folders for other ISE tools must all reside in the same directory.
Here's an example of an unsupported installation setup: