Change your project properties to add additional include directory paths for the preprocessor.
This can be done for an individual project:
Project/Properties/C-C++/Proprocessor. Here you can add many paths separated by semi-colons or use the convenient navigation ... provided.
Or fo all projects:
Tools/Options/Projects and Solutions/VC++ Directories. Here you can add paths for includes, libraries, source files, etc. Paths will be searched in the order they appear in the dialog box.
Then move your header files to the correct locations.
Rebuild.
Everything should still work.
FYI:
The preprocessor looks for #include <header.h> along one of these paths.
The preprocessor looks for #include "header.h" in current working directory (where your project files are located) first and if the header is not there, it reverts to #include <header.h>.
Personally, I woukld change all #include "filename" to #include <filename>. Then if you need to fiddle with the header you can make a copy of it, put it back in the project directory and change the include for that one file back to #include "filename" for your builds. When it works, copy the revised header back to its correct folder and change the #include back to #include <filename>.