Can I have two different versions of ChipScope Pro and switch between the two?
First, make sure that the %Xilinx% environment variable points to the same version of ChipScope Pro that you want to use. For example, you would point to ISE 6.3i, if you want to use ChipScope Pro 6.3i.
ChipScope in standalone :
You can run ChipScope Pro Inserter, Generator, and Analyzer if the ChipScope Pro version matches the ISE version.
ChipScope within ISE :
1. Open Project Navigator.
2. Go to Edit -> Preferences.
3. Select "Integrated Tools."
For ChipScope Analyzer, enter the correct path that points to the version you need, making sure that it is the same as ISE.