A good starting point is to enable JACK in the Projucer -> juce_audio_devices JUCE_JACK.
Setting this in the additional preprocessor-definitions of your exporter: JUCE_JACK_CLIENT_NAME=JucePlugin_Name will rename your JACK device (instead of just JUCE Jack or something).
For my multi-channel plug-ins, JUCE’s JACK implementation in the standalone host was quite limited, as it only forwards so many channels to the plug-in as the final output device (hardware) provides. That’s in general not so good when you go to a higher channel count e.g. with Ambisonics as an intermediate format. So I started writing my own Standalone application with JACK support, where each plug-in will open as many channels they need (however, the plug-ins in use have to #define their needed number of channels).
Far from perfect, but it works