If you want to autoconnect connections via JACK, you could use the JACK class from this SuperCollider quark:
So, if I want my setup be 'ready' for multirecordings, I can set each orbit to a different channel already (https://tidalcycles.org/index.php/Separate_audio_outputs) and connect them all to my stereo output of my soundcard. I need to re-connect to my DAW if I decide to record stuff of course (or let Ardour or NSM or ... do it for me), but this is just a example. (In the s.waitForBoot section I have it)
(
SCLOrkJack.connect("SuperCollider:out_1", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_2", "system:playback_2");
SCLOrkJack.connect("SuperCollider:out_3", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_4", "system:playback_2");
SCLOrkJack.connect("SuperCollider:out_5", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_6", "system:playback_2");
SCLOrkJack.connect("SuperCollider:out_7", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_8", "system:playback_2");
SCLOrkJack.connect("SuperCollider:out_9", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_10", "system:playback_2");
SCLOrkJack.connect("SuperCollider:out_11", "system:playback_1");
SCLOrkJack.connect("SuperCollider:out_12", "system:playback_2");
);
Seems to work here 
Other (Linux) tools for managing the JACK connections are:
- The Non-Session-Manager (NSM), using the client 'jackpatch'
- http://aj-snapshot.sourceforge.net/
- jack_connect via bash/your terminal
- Ardour does also restore the connections (and has NSM support).
