Unfortunately, the easiest thing to do is have a seperate DNN installation for each Portal, If you wish to migrate changes through different environments.
It seems that DNN is not built that way. It would be quite a project to create something to make these types of migrations possible.
It would be good because we are currently in the same situation, and have opted for the keep it simple approach, while it is definately not the most efficient, it will be the easiest to maintain, although upgrading DNN would be a chore once you have a lot of DNN installations for each web-site you are currently looking after.
I wouldn't know where to start, but simplest would be a Database name related to the portalalias which links to a seperate database that holds all the content for that portal.
Like I said, a big change for the DNN architecture. It is a shame that you can't execute code in web.config. that way you could point to different DNN databases depending on the domain name.