To me it sounds like every one of your pages is basically laid out the exact same with different content. For instance, you might have a left pane with navigiation a content pane with content and a right pane with Links. If you make a change to this layout you want it to occur across the entire site.
In my mind Dotnetnuke is dynamic in that every page can have a completely different look and feel from the others. Your approach seems very templated to me in that you want to run every page from one template and have it reflected. That sounds very rigid. However, no matter, that is just a semantic and not the point.
Like I said, someone who is savvy with the DNN database could achieve what you are looking for.
Just a few tidbits to get you pointed in the right direction. This is by no means complete, but it gives you an idea of what you are up against.
The "Tabs" table stores all of you pages in your dotnetnuke website. Every page is identified by a TabID, you will need to know the TabID for all of the pages you want to change in mass.
The "DesktopModules" table stores all of the modules you have installed on your webiste and assigns each a DesktopModuleID.
The "Modules" table stores a list of all of the module instance on your website. Each instancehas its own ModuleID and is tied to the DesktopModules table by the DesktopModuleID.
Finally you will need to leverage the "ModuleSettings" table so that you can get all of those settings values you stored with your module you created.
You would basically create a bunch of new modules table entries and modulesettings entrys, along with TabModules entries to massively place/remove modules from pages.
You are going to have to spend some time with the database to get initimate with it. You should 100% definitely do this on a test site at first. Add a page, add modules to the page, observe the changes in the database. Delete a module oberve what happens.
Another idea, and this isn't really in my realm of expertise is basically convert the modules somehow to skin objects (I am not sure this can be done), but anyway basically your skin will automatically have all of the modules in place and a simple skin edit would allow you add/remove a module. It might not be doable, but perhaps some wiser than us knows about it.
I really hope that helps,
Stuart