The difference between binary and source is that binary has no C# source code. All the code is compiled into dlls in the bin folder beneath the root of the web. This is the best practice for production servers and pretty standard for ASP.NET projects using the code behind model. You don't want to deploy source code on production servers as this is potentially a security issue and source code is not needed on production since everything is pre-compiled.
If you want to learn ASP.NET, I think mojoPortal is a good project to study as the source code is well organized and very readable (at least in my opinion
I recommend that you get the source code from svn rather than the .zip
Read the documentation starting here for more info:http://www.mojoportal.com/developinginvisualstudio.aspx
It would be good to get a book on ASP.NET as well, though there are a lot of good online resources.
Whenever I find sites or pages of interest for ASP.NET I bookmark them here:http://www.joeaudette.com/aspnetlinks.aspx
Hope it helps,