Hi
Firstly for the passwords, are you using the SME server's server manager to do this?
Secondly I think the admin account is used for either viewing the server status [Blue status screen] or performing admin operations on client machines.
If you want to run scripts or use the command line, you should login as root using putty which is an ssh client.
You should enable root access by using the Remote Access option under the SME server manager before using putty.