Yes your disabled APU integrated graphics goes through your motherboard's Video Outputs.
When you installed your GPU card than you need to connect all your Speakers and/or Monitors to the GPU's video Outputs to get video and audio.
You might be able to use both. See what happens if you enable your Integrated Graphics again in Device Manager with your GPU installed. Your GPU will still be the Main Display adapter used by Windows but you might be able to use the Integrated Graphics also as a backup in case something goes wrong with your GPU card.