Hi,
You do ALL configuring of the SMEserver (in terms of user access - ie Windows shares etc) through the server-manager web site.
Sometimes you need to connect to the server either directly (ie at the server keyboard) or using a terminal program (like PuTTY). You login as root, with the admin passsword, and run the "console" program - see the manual for this.
However, remember, 99% of what you want to do is done through the server-manager.
Cheers
Ian