I have a responsive template which requires a particular footer container and I want to use another container for the content areas.
As far as I can see you can either set containers at page or module level, not both.

As the footer will be on every page of the site I do not want to set this manually on every page module.

 Thanks Michael, that seems to have worked a treat. I have set the panes to the containers I wanted in both the footer and content areas and any new pages using that skin auto pick up the containers.

The inability to assign modules/styles to menu options like Joomla for example, is the only drawback in DNN. I hope I never have to re assign modules from page to page accross a whole site in the future.
I assume it could be done in the database so if anyone has a query for this or a pointer as to which tables I should look I would be grateful.

Sorry Michael , what I was really meaning was the assignment of Modules.

Many CMS's let you assign modules sitewide by selecting a checkbox against the menu items for the pages they need to be on, If you then need to change the selection list it is a simple procedure to select or deselect from the list.
I shudder to think how much work DNN would be, if for e.g a local goverment site decided to hide modules from half its pages or add a new module to the sidebar for a say a couple of hundred pages.
We are actually evaluating whether DNN pro could be an alternative to our commercial CMS for our local goverment sites, and this lack of sitewide management may well go against DNN.

I suppose you would have to create specific skin ascx's to handle the different layout options of often repeated elements.
Can a module be added to a skin file direct??, if yes that might be an option.