Currently the extension always overrides the workspace settings if a workspace is opened. Because of that linters can not be set manually by an user.
An option to deactivate the extension for a single workspace (or through the global settings) should solve this problem. The action to automatically set linters through the command palette should still work though.
Right now the extension just checks for a .jscsrc file.
JSCS can be configured in a package.json file under the jscsConfig property though or the configuration can be located in a .jscs.json file.