I have been looking for books that may appeal to your question, and I must say that I have been a bit disappointed in what I have (or have not) found! There are, of course, a plethora of corporate titles that will tell one "how to manage," (hierarchically) and there are many lefty publications about activism, but few that are written by activists or radicals about how their cooperatives work (that I was able to find).
I browsed through a few library catalogs and bookstores, and was only able to find a few titles that looked like they might touch upon your question:
Rules for Radicals by Saul Alinsky
The revolution will not be funded : beyond the non-profit industrial complex by Incite! Women of Color Against Violence.
Organizing for social change : Midwest Academy manual for activists by Kimberley A Bobo; Jackie Kendall; Steve Max; Midwest Academy.
Tools for radical democracy : how to organize for power in your community by Joan Minieri; Paul Getsos.
Building powerful community organizations : a personal guide to creating groups that can solve problems and change the world by Michael Jacoby Brown.
Some of the subject headings that might be useful for searching for other titles:
Community organization -- Handbooks, manuals, etc.
Social action -- Handbooks, manuals, etc.
Citizens' associations -- Handbooks, manuals, etc.
Community development -- Handbooks, manuals, etc.
Organizational effectiveness -- Handbooks, manuals, etc.
This doesn't mean that there may be more resources in journals, magazines or online. Since I am also interested in this topic, I will keep searching and share what I can find here. Hope this helps, Adam! If this is all way off, let me know and I can try further searches.