Hi and thank you for your question/suggestion. A user manual is not forthcoming at this point. In its stead, we already have:
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The help index, which indicates help resources already available
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Google using "site:mididesigner.com" in the search field (or "midi designer" in the search field). Most of what you're looking for is out there.
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This Q&A site, where the community responds quite quickly to questions
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The contact form, where I can be reached directly and I answer even the most basic questions fast
In addition, a devoted MIDI Designer user (Chris Gretton) and I will be collaborating on a Mechanics Layout Book, which will show a lot of MIDI Designer use-cases either through pages or via entire layouts. This might take a bit to get moving, but it should cover a lot or all cases of supercontrol-subcontrol relationships.
At the same time, I feel your pain regarding not having a single source to read, study, and learn MIDI Designer. Right now, however, with my resources torn between pushing the product forward (so much to do!) and documenting what we've got, I'm going with the former.
If you'd personally be interested in working on a Getting Started Guide or a User's Manual, you would count with my full support, of course.
My dream is that somebody swoops in a writes an Idiot's Guide to MIDI Designer, but my idle dreams don't help you today in learning MIDI Designer. The only thing I can say is: Dig in with what you've got available and ask the rest. I'm glad to help.
Thanks again for your question and your patience in learning MIDI Designer.