"Use the commercial files along with the newer Dark GDK files" seems to be a misunderstanding. For Dark GDK, there is no difference between "commercial files" and "free files". The difference is only the license. If you have a commercial license, then you can sell the games you make with Dark GDK, otherwise you can't sell them. But there is no difference in files.
The original Dark GDK installer installs the original libraries and headers, and some extra material: tutorials, help, models to experiment with, etc. The updates replace the libraries and headers that are actually needed to compile a Dark GDK program, while they don't contain or replace any of the extra material. So you can either overwrite the libraries/headers with the downloaded update, or put the update files in a different directory and set the compiler directories to the latest version. It's possible to have several versions in different directories and you can change with which of them you want to compile.
For Dark GDK .NET, AFAIK there is only a commercial version, so again it's easy, there is only one version. (But I don't use it so correct me if I'm wrong.) Quotation from here:
http://www.thegamecreators.com/?m=view_product&id=2128&page=upgrade
"Dark GDK is freely available and requires a commercial license if you wish to sell games. Dark GDK .NET on the other hand is not freely available, however, when purchasing it comes complete with a commercial license."
Regarding the "most recent compiler..." question: Dark GDK was designed for MS Visual Studio 2008 (which version of 2008, Express or Professional, it doesn't really matter). In the latest update, libraries for MS Visual Studio 2010 were provided and there are now (at last) setup instructions as well, but the plugins might not be compatible with that. Which plugins work with a newer compiler and which don't, I guess you can only find out by trial and error. At least I haven't seen information or a list about plugin compatibility yet, but again, correct me if someone knows better.
Dark GDK .NET is not sure to work with VS 2010, but the .NET version has its own forum and I guess you'd better ask on that forum what is the current status of the product.
http://forum.thegamecreators.com/?m=forum_read&i=37
You'd also best ask in the Dark GDK .NET forum whether it is possible to use plugins meant for Dark GDK from .NET language or not, and if yes, how. If you can't get an answer on the other forum, you can also try to send an e-mail to TGC about it.