Right click on the Jack Control icon on the right hand side of the Menu bar and select 'Connections'
In the Connect Panel, select the ALSA tab and make all the MIDI connections that you need
Test these connections in jOrgan to make sure everything is working
If you are using an external reverb (Jc-Gui or Jack-Rack), then click on the Audio tab and make all the audio connections needed.
Test to make sure that everything is connected as you need it to be
Right click on the Jack Control icon on the Menu bar again and select 'Connections' again to close the Connections window
Now right click on the Jack Control icon again and select 'Patchbay'
In the Patchbay Panel, click on the 'New button'. This should open a dialogue box asking if you want to create a patchbay definition snapshot of the actual client connections
Click on 'Yes'. This should automatically replicate your connections in the Patchbay
If the Save button is not enabled, remove a MIDI or Audio device from the patchbay that is not being used (for example, MIDI-Thru)
Once the 'Save' button has been enabled, click on 'Save'
Enter a name for this patchbay in the File name box
Click on 'Save' within the file dialogue screen
Click on 'Activate' back in the Patchbay window
Close the Patchbay screen by right clicking on the Jack Control icon and selecting 'Patchbay'
Now open the 'Setup' screen by right clicking on the Jack Control icon and selecting 'Setup'.
Click on the 'Options' tab and make sure that the 'Activate Patchbay persistence' check box has been enabled and that your patchbay file is listed in the patchbay drop down.
Click on the 'Settings' tab of the Jack Control Setup window and Save your setup (If the 'Save' button is not activated then de-select and re-select the 'Realtime' check box and the Save button will activate).
Close the Setup window
For more information and other options on how to use the Patchbay, see http://www.rncbc.org/drupal/node/76