Do you have the .mu plugin?
If you do then it depends on whether you just want them to appear lit up or if you also want them to cast light as well.
For just appearing lit up then if your models material set up uses the KSP emissive set up, scroll down the materials section till you get to the MU Shaders section and then click on Shaders. It will open up a list with all the various types of KSP shaders. Pick KSP/Emissive/Diffuse. Once you have done that make sure you give it a name or it won't save. Then below that there is a texture section with 2 texture pic sections "_MainTex" and "_Emissive" When one is highlighted, below it is a section with the name and just below that is the name of the picture you set for your main texture(you have to make this outside of blender with a paint program.) You need to edit it to say the name of the texture pic you created(it does not need the suffix). With _Emissive highlighted do the same but edit it to be the emissive pic you created. An Emissive pic should be a duplicate of the main texture, darkened to pitch black but with the sections you want to light up, brightened to almost white. When you UV map your model you will have your windows over these light sections.
When you config your model add in this module and you will have the toggle in the UI to turn lights on and off.
If you want to cast light as well on the same toggle you need to study the new KSP stock lights along with their config files to see how it is done. If you get stuck then let me know and I can try to clarify stuff you get stuck on.