After loading a user message into a thread, after configuring an assistant, you must invoke a run with the assistant and thread ID. You must then continue polling to wait for a reply to be ready.
Documentation and API reference are two links in the sidebar on the left or menu of this forum. Each have a section for assistants.
In order to keep the status of your run up to date, you will have to periodically retrieve the Run object. You can check the status of the run each time you retrieve the object to determine what your application should do next. We plan to add support for streaming to make this simpler in the near future.