>If I am in /user/X11R6/bin
>
>and i type:
>
>xterm
>
>I get:  command not found. I have to type:
>
>./xterm

Yes, this is a problem with your path statement.

I assume you mean /usr/X11R6/bin/, not /user/X11R6/bin.

Check your path variable.  What shell are you using?  If you're using 
bash or a different shell then you're going to need to change a different 
rc file.  Also, when you try and run xterm, are you running from root? 
because when you 'su' to root your path variable will change, so check 
your .cshrc in your /root directory.

-Andy Sinesio