ok assuming you downloaded FAH504-Linux.exe
To use this program, make sure that you can execute it (chmod +x FAH5-Linux.exe) and then run it ./FAH5-Linux.exe
basically all you have to do.
but! run "./FAH504-Linux.exe -configonly" then you can input your name, team number, etc. Unless you're going to be running 2 clients or want to crunch heavier work units you can just hit enter to everything after those two.
our team is: 76140
then just type "./FAH504-Linux.exe" and you should be good to go. I use the " -configonly" tag in case I forgot something I don't want to have to hit ctrl+c and run it again you know...but whatever.
I don't have mine set to start at system boot but you probably could, I haven't really bothered to look how...
If I missed something or whatever just ask.
and read this: http://folding.stanford.edu/console-userguide.html