What does the checkbox for some apps in iCloud > Options > Documents mean?
Firstly, the checkbox for Mail just means it syncs Mail.app settings via iCloud and also it enables the iCloud Account in Mail.app or turn it off. 

Secondly, System Preferences settings are also synced via iCloud, for example iCloud syncs my preferred Wifi to any new iOS or Mac I enable iCloud on.

Likewise Weather locations for any city you setup is synced over iCloud.