If You use MS Visual C++, it is one way, with Borland it is another way, with X-Windows - another way etc.
Do You wish to use MFC? VTK? Dou You wish to visualise with Direct X? Open GL? Bitmaps and DCs? There are too many cases, nobody can say You, what do You have to do.
There are no best way for all cases: Direct X is quicklier, but not easy. X-Windows can be used with another OS (Unix) too; VTK is powerfull, but not easy for beginner etc. I would say, use Open GL for Your 3D.
The best way, look Win32 graphics samples on MSDN and decide, witch technique You wish to use, and then take a part from the sample for Your program.