When you set the UVs for your model, make sure the faces which are supposed to have a different material get assigned to different images. When you then import the model into Unity, you will have a different material-slot for each image in your model. You can then drag-and-drop different materials into those.
Another option is to use one material for everything and add an emission texture to it. Make that texture black except for those parts of the texture which are supposed to glow. In that case you don't need any specific geometry in your mesh just to define the emissive parts. You can do that with the texture. Here is an example for such an emission texture from the Unity documentation: