For me, it really depends of how high the tech level is, and how large the ships I'm building at the moment.
If playing conventional start and/or at low tech level, I generally make an entirely new design. Since the ships are still small and the tech level is low, I feel that I need to make a dedicated design. Usually, aside from the flag bridge, I fill it up with defenses (armor, PD and/or AMM..) and sensors. This is because I feel that ships are fragile enough at this point, and the lack of space means the ship would have rather low offensive capabilities anyway. So, better to make it as sturdy as I can with some added missile defenses that can benefit the whole fleet.
Once ships become larger (15000+ tons) and tech level rises (which means more miniaturization) I'm free from these constraints, and I either roleplay or build what makes more sense, depending on the game. This generally means taking my largest warship and doing some modifications to the base design.