While I'm sure I don't understand all the details of your situation, I suspect that understanding the construction of themes a bit would probably give you the answers to your questions. Each theme has it's own folder within the "themes" folder
that is in the root folder of the Blogengine.NET application. Inside that theme folder is the site.master for that theme that defines the layout.
Al Nyvelt has two "how to's" that would seem helpful for you. One is on making different pages look differently:
The other is his "Non Zero" theme that you can examine as an example of using different numbers of columns and styles:
In a very simplistic way, you can always construct a link that will open in a particular theme by appending a little querystring information.
So, for example, (still using Al's blog as an example), you could open his front page in the standard theme with this link:
Adding the ?theme=standard even after a long "post" url works, too.