Thanks for this - Ah ok...sooooo, if I have this right.
When a site is cloned for the first time from the one you decide is a template, then all of those sites share the same *theme*...I guess that makes sense.
Now along comes a new install - the granddaddy one that is going to aggregate categories into a shared blog, for example' using something awesome like WPMUDEV's Autoblog - https://premium.wpmudev.org/project/autoblog. Now this one is going to *look* the same as the clones but have different widgets and things. Essentially it uses the same *theme* - not literally sharing the theme, but I suppose it can have its own version of the theme.
1) Create all themes that want to be cloned and mass tweakable from a template blog
- edit template blog and all of its clones share the same theme, this one tweak to the template updates them all.
2) To create the granddaddy blog - do a fresh install of a blog and then install the theme all by itself, afresh.
- edits to this blog's themes are only applicable to itself, as one would expect.
This I do suppose would mean that the theme files live in one place where they can be hacked up for the clones, and then also a different set the theme files lives in the granddaddy blog's theme folder.
So for all intents and purposes the clone site share the same themes folder in the templates blog's themes folder, and the granddaddy's theme lives in its very own themes folder.
The granddaddy blog then sucks in certain things from the clones into what looks very much the same as the templates blogs, but with it's own bespoke tweaks and settings.
If this is the case it makes sense and its almost so obvious I'm almost embarrassed to have asked.
If this isn't the case I'm more confused now than I was before!