Its such a broad question that there wont be any docs for it. Its seams more like the outline for a project than a question really.
"We want to create a quota for our commercial users and create a walled garden for them inside the main site."
You want some pages that can only be accessed by users in a particular quota, yes that can be done, every page built with Site Builder can have its access set, so limiting to a particular quota is one of the options.
Docs: "What is Site Builder?"
https://www.jamroom.net/the-jamroom-network/documentation/site-builder/2634/what-is-site-builder
"We want to put this behind a paywall using Paypal payments or our Shopify system if needed."
You want to use Paypal or Shopify.
Paypal is a payment gateway accepted by 2 modules, Foxycart and the "Paypal buy it now" module. Only the Foxycart module is capable of selling subscriptions. You can use that to sell subscriptions that change the user into the quota that can access the garden. Or you can sell that directly to non-members.
Shopify is a cart system and no module exists to bridge it to jamroom currently.
"This area would allow access to special videos, documents and forum areas not accessible to our regular community."
Seams like you should setup one profile in its own quota maybe call it 'garden', then give its quota access to those modules: Video | Docs | Forums, then set that profile's level of privacy to "Shared - Profile owners and followers only"
Or you add a bit of code to the skin to check that the viewers profile was in a profile allowed to view and redirect if not, similar to this setup:
Docs: "HowTo: Make the site visible to members only"
https://www.jamroom.net/the-jamroom-network/documentation/jamroom-admin-handbook/4357/howto-make-the-site-visible-to-members-only
There's a few ways to approach the setup.
"Can we use a different skin for this area,"
Yes, the Profile Tweaks module will take care of that.
Docs: "Profile Tweaks"
https://www.jamroom.net/the-jamroom-network/documentation/modules/2910/profile-tweaks
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