I want to know what difference is 'Site Master Page' and 'System Master Page'. I find it here in this tutorial,
Site Master page is the default master page you and your end users will see in your your site collection. System master page is the master page used in the Sharepoint system pages like in 'Site settings' (mostly the sharepoint pages in the Layouts folder).
If you go to /_Layouts/ChangeSiteMasterPage.aspx of your site collection and change the system and site masterpages to alternate masterpages, you'll see the difference.
go to http://yoursite.com/ : this is using the Site Masterpage
go to http://yoursite.com/_layouts/settings.aspx : this is using the System master page