What I normally do is pick and copy the most expensive design (colonizer is good for that), reduce engineering and the endurance to the minimum (1 day or less for non-civ), put the most expensive (cost per ton) components of the other designs I want, and/or the components that many designs have in common, and then tinker around. With military ships, expensive weapons are often the way to go. For civilian, putting some colonizer modules can help. Often the biggest problem are the engines, if the other designs use different ones.