when you go on http://www.xilinx.com/support/download/index.html/content/xilinx/en/downloadNav/design-tools.html you should download the full installer for your OS in the middle of the page. The license setup should be proposed after installing the tool. Can you share a screen capture of the tool you launched after installing ? Are you sure that you executed ISE and not the Vivado tool ?
maybe the wiki is not clear on this point, but the pre-configured image is already fully configured and tested so all the steps described in the wiki does not apply. These steps are to be completed if you start from a stock raspbian image. I will complete the wiki to make that point clear.
It seems that we will make our way to the official beaglebone kernel, so expect the upcoming Debian/Ubuntu/Angstrom distribution to include logibone support !
Tell me if you have any problem running the debian image, i tested it created/tested it today so you are a beta tester on this.