You need to create a second UV set in your modeling software. You should use automatic mapping for those UVs in there. When you import your mesh in Unreal you should assign the second UV slot to the lightmap. Second UV slot has the index of 1 while the primary is 0.
Automatic lightmap generation isn't as good as doing it by hand. I might work for some assets, but there is going to be other assets where you will have to do it by hand to get the best results. Also knowing how light maps work can help you make better low poly models and modular models for UE4.
Lightmaps can be a pain... Check out this tutorial, it shows you how to enable the LPV feature (still in beta btw). All realtime lighting. :) https://www.youtube.com/watch?v=Oni6TG2DXnk