Is there a way to avoid the tedious manual model layout I have to make after reverse engineer?
You can save the layout of your model by going to Model menu | Layout and clicking Save. After reverse engineering a changed database, you can load the saved layout into the new model and will easily see the new items that you can re-arrange as desired.
NOTE: Some logical information can be lost as it may not be saved within the Layout. We recommend you to test it whether this possible method will suit you.