1.

There is a small icon above the solution explorer that has a tool tip of "Show all files". Click it to see physical files on disk instead of the filter view.

Then right click any files or folders to "Include in Project" or "Exclude from Project"

2.  How to set per-configuration defines to conditionally #include code.

I suggest you put conditional code in .h and .cpp files then #include the correct functionality conditionally using a compiler #define.

For example in the Visual Micro project properties you can set configuration specific compiler defines myDefine=foo;myDefine2=bar

#if myDefine == foo
   //some code
#endif

or easier still use the configuration specici "_DEBUG" project property. ie: Set _DEBUG to 0 or 1 when Release is selected and set it to 1 or 2 when Debug is selected. Then in your code use

#if _DEBUG == 0
#if _DEBUG == 1

Or just set the _DEBUG property for the Debug configuration and test for the define

//release
#if !defined(_DEBUG)
#include "myheader1.h"
#endif

//debug
#if defined(_DEBUG)
  //some code
#include "myheader1.h"
#end if


I recommend external h/cpp but you can wrap any code in the .ino sources using or one more #defines. Code can get out of control very quickly and be difficult to read. 

As far as .ino files are concerned all the .ino code will be compiled in one "combined block", however code in #if conditions will be ignored by the compiler. 

For cpp/h files if a header file #include is wrapped in a #define, then the related .cpp file(s) are not passed to the compiler or linked as objects.

You have to wrap the code with an #if

examples are in my previous comment.