It helps to understand that, as far is MODX is concerned, settings are just settings. When parsing a page, it doesn't even know where they came from. If you use a setting tag:
You'll get the value of a User Setting if one with that name is set. If not, you'll get a Context Setting if one with that name is set. If not, you'll get the System Setting.
IOW, User Settings override Context Settings and Context Settings override System Settings.
Technically, before parsing any tags on a page, MODX loads the System Settings, then it loads the Context Settings (which will overwrite any System Settings with the same key), then it loads the User Settings for the current user (which will overwrite anything already loaded with the same key).