glBindVertexArray(vaoId);

// ... tell OpenGL to draw on first window

glClear(GL_COLOR_BUFFER_BIT);
glDrawArrays(...);

// ... swap first window buffers

// ... tell OpenGL to draw on second window

glClear(GL_COLOR_BUFFER_BIT);
glDrawArrays(...);

// ... swap second window buffers

glBindVertexArray(0);