I don't know how to set a capability in Botium Box.
Most important capability settings are part of the Botium Box UI.
For custom capabilities or special capabilities not used very often, you can add the capabilities to the capability list in Botium Box.
A Test Project has a Capabilities & Envs section. Those are used whenever this Test Project is started:
Set the Connector/Chatbot Technology field for a Chatbot to Other (Advanced Settings) to reveal the capability list: