Hey Fenes, the model is looking good so far!
If you find it easier to unwrap everything separately and combine later, that can work just as well 👍
My only guess for why it would look different after finishing the unwrap is if you accidentally changed the number of vertices while unwrapping (edge sliding and removing doubles, etc…). Beyond that, unfortunately, I don’t know. Thankfully Blender 2.8 will allow multi-UV editing by default, so this should be much easier in the future.
