A common way of doing this would be to #define something (or not) in your .ino file before including your .h file
.ino
#define USE_VERSION_B
#include "lib.h"
...
void setup() {
...
and then in lib.h
#ifdef USE_VERSION_B
// define everything you need to
#else
// define regular stuff here
#endif
Note: This #define does not carry over to your .cpp file. That file is compiled separately from your .ino file and then they are linked together. If this creates a problem for your library, you can either insert all your code into the .h file (some libraries do this) or have some sort of library .begin() function where you would pass an argument to do option A or B.