The first section in the config is for the Microsoft ASP.Net providers. (These are provided from Microsoft and have some useful features.)
see: http://msdn2.microsoft.com/en-us/library/6e9y4s5t.aspx (The 'MS Providers')
The second config section is for Charles Nurses custom DNN membership providers.
which seem to use a lot of the same methods as the Microsoft Membership Provider, along with some extra functionality needed by DNN. (The 'DNN Providers')
Overriding/rewriting the DNN Providers (the second one) and plugging your re-written/overridden versions of these classes into DNN seems to do the trick, if you look at the code for the original DNN Providers, you can see that they use a lot of the functionality of the MS Providers. as in some of the methods call methods in the MS Provider.
Such as generating passwords, ensuring the password meets the configuration of the MS Provider. (min/max length/non-alphanumeric chars) , I think it is also used for authenticating the user as well.
It would be good if authentication and unauthentication could also happen in the DNN Providers. Or maybe some event delegates like On_Authenticate and On_LogOff
I've kind of done the same with my new DNN Providers which I based on the original DNN ones but rewrote the code where needed, to plug in our own functionality/data structure.
Hope this helps.