Call glutCreateWindow for each window. Window size and position can be specified with glutWindowSize and glutWindowPosition prior to glutCreateWindow. Calling glutCreateWindow multiple times effectively creates multiple OpenGL contexts, meaning that you need to properly initialize each context after calling glutCreateWindow. In particular, take care of buffer objects and textures. Those created with a context cannot be used with other contexts.
OpenCL context created with an OpenGL context bound for the inter-operation can neither be used with other OpenGL context which are not bound to OpenCL context (need to be proven).