Enabling is done through the "Command Configuration" APIs. It's at the top of the swagger page under command-configuration-rest-api. (And I apologize in advance, because this is a pretty rough area of the Container Service's design.)
First, for reference, there are wiki pages describing how to do this through the UI:
Enabling Commands and Setting Site-wide Defaults and
Enable a Command in Your Project. The API works exactly like the UI does. You can configure a particular command wrapper at either the site or project level—where configuration means setting things like default input values or matchers for things like scan types and so on—and you can enable/disable each wrapper at the site or project level.
To use the configuration APIs you'll need either the wrapper ID of the command wrapper you wish to enable or both the command ID and the wrapper name.
To enable sitewide, PUT to /xapi/wrappers/${wrapperId}/enabled or /xapi/commands/${commandId}/wrappers/${wrapperName}/enabled.
Similarly, to enable on a project PUT to /xapi/projects/${projectId}/wrappers/${wrapperId}/enabled or /xapi/projects/${projectId}/commands/${commandId}/wrappers/${wrapperName}/enabled.