[chef] AWS OpsWorks custom

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I'm using AWS OpsWorks for a project.  I think most of my cookbooks will not
require modification, and I can just use the ones from
http://github.com/opscode-cookbooks/
I expect there will be some of those I will need to modify and perhaps will
need to create some new ones. 
(For example, I would like to use the django recipe, but want to substitute
uwsgi for gunicorn.)

I'm a bit confused on how to structure this.  I believe I need to point my
OpsWorks stack to a github repo that contains the cookbooks.  That's done in
the stack configuration:
"Use custom Chef Cookbooks"
OpsWorks requires the repo to be structured like this:
http://docs.aws.amazon.com/opsworks/latest/userguide/workingcookbook-installingcustom-repo.html

I've seen some mentions of using git submodel to incorporate the required 
repos
in a "parent" repo.  I've also read that that practice is deprecated.  What
*is* the best practice?

I've looked into Bershelf and Librarian-chef, but don't see an easy way to end
up with the required directory structure while still being able to add new
cookbooks and modify the existing ones.  I'm trying to avoid just making a 
copy
of the cookbooks.  I think I also need to make sure dependencies can be
satisfied.

Can anyone give me some tips for a sane OpsWorks/Chef workflow?