Using the example of the ManMachine1 program (part of the Man Machine multi). You can view it as a program that has two distinct patches going in parallel: The main melody (Osc2, Flt1, Env1, Env2 and Output1) and the bass line (Osc1, Osc2, Flt2, Env3 and Output2). In this article I'm only focusing on a single program, not a Multi.
Photo1 shows the patch - you can see that it has two outputs (one for the main melody and one for the bass).
Photo2 shows the first sequence (Subsequence 1), which is for the main melody. The "pop-up" window you are seeing in this picture is the one you get by clicking the Connect button. The parent sequence (which has three subsequences) assigned to this program is I12, on my Origin (this will probably be different on your Origin). The Trig1 trigger goes to Env1 and Env2, which drive the main melody's Filter (Flt1) and VCA (output1). The sequencer step voltage (Out1) goes to the main melody's oscillator Osc2 (it is a single oscillator sound). Note that if you open up Osc2's FM input, you'll see that it is also controlled by the keyboard - so that the key of the sequenced melody shifts when playing different notes on the keybard. The Accent1 output goes to the bass sound's filter (Flt2) This was an oversight on my part (since I'm using Seq1 for the main melody) but in this case none of the Accent steps are turned on, so it doesn't have any effect anyway. But if you do switch some of the Seq1 accent steps on, it will accentuate that step in the bass line by opening the filter with the simple AR envelope the Accent function offers. I can use this "wiring mistake" to illustrate the fact that you can have any of the three subsequencer's (Seq1 , Seq2, Seq3) three outputs (Trig, Out, Accent) go to any module, no matter which "sound" it belongs to.
Photo3 shows the second sequence (Subsequence 2), which is for the bass. The Trig2 trigger goes to Env3, which drives both the bass sound's filter (Flt2) and VCA (output2). The Out2 sequencer step voltage goes to Osc1 and Osc3 (the bass sound uses 2 oscillators).
Photo4 shows that Seq1 (main melody) and Seq2 (bass) are activated.
One thing that is not obvious when working with the sequencer is that in order to change things in any of the 3 sequences in a program, you have to hit the Edit button (on the right of Photo4). Otherwise the sequencers are in "performance" mode, which is a whole different subject.
In this particular example, you have two subsequences driving two different instruments / melody lines. For programs where I have multiple parts like this going, I usually always have the program set to one of the "Mono" modes (Mono Low, Mono High, Mono Last) in the performance page, which unfortunately I don't have a screenshot of here. Note that in an origin program, Mono doesn't necessarily mean that you can only have one melody line/instrument, it just means that you don't get chords when pressing down keys. Even though you are in Mono mode, you can still have four different instruments - perhaps three driven by the three sequences, and the fourth played on the keyboard. You can have instruments in a program that don't respond to the keyboard at all, by simply removing all trigger connections in the envelopes and FM connections in the oscillators, filters, etc. that come from the keyboard.
You could also create a program with just one instrument, where each of the three subsequences have a different function: Seq1 for trigger and oscillator pitch, Seq2 Out for filter cutoff, Seq3 Out for envelope decay and release times (just one example).
Or you could create a one-instrument program with three oscillators going through the same VCF and VCA (using Mixer), but with each of the subsequences controlling the pitch of each oscillator, and only Seq1 controlling the envelope trigger. Basically a three-part harmony patch driven by the sequencer (I could see this yielding fun results, especially using each subsequences Random button...). And, as before, this program can still be in Mono mode. even though you have triads going on, driven by the sequencer.
Since the design is that of a modular synth and sequencer, I'm sure you could use the sequencer's outputs, triggers and accents in really perverted ways that no one has thought of before!
Let me know if you have any questions...hopefully I haven't caused even more confusion.