I don't think the root directory is the best place to add this program. Manually added programs are usually best placed somewhere like /usr/local/bin. But hey, it's up to you.
Environmental variables are user-configurable settings the shell uses. In bash you can set a variable with VARIABLENAME="variable_setting"
. So what you need to do is run:
Now you should be able to run the program in that shell. You can run the 'env' command to see a list of the variables you have set up. Note that an environmental variable will only be set for that shell, and it will be lost when you close the terminal. You have to place the lines in your ~/.bashrc or /etc/bashrc (for global access) if you want to make them permanent.
Other shells, like the csh you mention, should have a similar syntax but may not be exactly the same. Check the shell's man page. If you don't know what shell you're using, it's probably bash, since that's the Linux default.
Note that the xcConfigure program will do all the above for you, including adding the variables to your bashrc. So I suggest deleting everything and starting over, and run xcConfigure first. Only fall back to setting it manually if nothing else works.