Didn’t see a response to this so thought I’d reply in case you still don’t know 
Yes effects units with MIDI CC capabilities can have instrument definitions - you can assign each parameter and label it - and then have pages of the devices parameters available in the track values page for the fx unit.
Eventide H9 for example then becomes a playable device beyond the actual units single knob.
But equally as handy is that you can then assign a pattern to the track and quickly design automation on any MIDI CC and know what each MIDI CC is without needing a manual to check, as they are still labelled from assigning them as track values.
Push wet up everytime you reach the end of 64 bars - takes 10 secs to create a pattern. Change delay time every 7th 16th - agin very easy to do. And can then use another track assigned to the same instrument and automate another parameter and so on and so on…
(A note on H9 is i set up one for delay algorithms one for reverbs etc etc, that way the instrument definitions are labelled with algo relevant terms as MIDI CC xx is say delay time or reverb something or chorus something else depending on algorithm)
Re: MIDI INs (remember can use USB as a MIDI IN from your DAW for example too)
I have a master keyboard - all other synths connected are set up to be ‘edtrk’s so can all be used to input note data into whichever Cirklon track is selected, and also a Tempest as another MIDI IN if wanting to play Rhythms from its pads.
MIDI IN can also be used to transpose everything playing from the Cirklon, and can also be used to change Cirklon’s scenes.
You can also re-route internally so devices connected to Cirklon In can also send MIDI data to devices connected to Cirklon MIDI outputs - perhaps decide one day to use Octatrack arp to sequence a synth usually sequencer from Cirklon for example.
In terms of multi timbral instruments like your Digitone example.
When you create an instrument definition there is a check box for making it a ‘multi instrument’ this will then treat it as a multi timbral instrument - and to the right of its name in the track page there will be a number which indicates which MIDI channel is playing. You can highlight this number and change it, and also when you assign the same instrument to another track it will set it to the following MIDI channel to save having to do it yourself.
The handy part about this is that the MIDI CC labels are done once and apply to all MIDI channels - as if you assign an instrument def to each mid channel you will need to either do the labels again manually on the machine, or by using a text editor copy and paste into each channels instrument definition. Not a massive deal but doing it once on the machine is generally my choice. Exception is drum machines that have different parameters per voice - such as Jomox or Tr09 say - that way I’ll have a inst def for each voice - as once the Jomox snare is assigned I can quickly access the parameters relevant only to the snare on the track page rather than having to scroll through pages of the whole machines parameters.
The other factor to consider with the Cirklon is what they call Force to scale (FTS)
This means that you can set it to on for sat a synth and you can transpose the whole scene and it’ll stay in scale rather than just a raw transposition of all notes it’ll make notes sharp and flat where needed to remain true to scale. And this can be on a track by track basis. Super useful but it’s relevance here is that for rhythmic based things you probably (although can still have uses if drums are tuned…) don’t want you drums being transposed as generally it’ll push say the kick notes up so that it plays a snare instead for example, so for rhythmic based things you’d generally turn FTS to OFF in the instrument definition. But the need for duplicates arises if you use the device for rhythms and music - such as a sampler.
So I have the exact same instrument definition labelled with FTS at the end and use this for music and other for rhythms. For example:
Akai S950
Akai S950 FTS
In terms of sequencing on the machines or not. I went through a stage of doing everything on cirklon apart from elektron machines - then all through Cirklon as doing longer patterns is just easier this has the added benefit of meaning that as pattern data isn’t saved in the Elektron you can use patterns on DN/DT/SN as AR/A4 kits… unexpected benefit.
Currently I’m doing all of the above - it’s been good to work in both ways as makes it fluid and keeps it fresh as can work whichever way I fancy on that day - and utilise the options as best for track. But generally Cirklon does most heavy lifting as I’m into structures and placing fills across long periods of time and it’s just easier for me to achieve that with Cirklon the quickest.
Hope that’s useful.
