Ship Design Management.
from
GalCiv2 Forums
I thought I would point out a few things I do to keep all my ship designs in order and dodge a few bugs. 
When I design a new ship I always make a prototype. This means I make a ship that is only a hull and extras.
When I wish to make a production run ship I "upgrade" the prototype, change the name, and add weapons and engines etc.
This should help avoid an elusive bug involving upgrading ships and being unable to change them or unable to remove certain parts. It also meens no more removing old parts should you choose to upgrade a fully equiped ship.
Also your prototype designs will be visible as soon as you get the hull tech; the best reason to do this!
I also label the ships in a way that is easy to track on the list.
A-NAME-M[x]
The first letter is A-E. Each letter represents a hull type from Huge to tiny. I use U for Constructors and Transports.
The next is simply some fancy name for the ship and the last indicates its Mark.
A-X-NAME
This is the Prototype listing. It obviously forces the prototypes lower down the list.
Until the game has a better way of organizing the ship designs, I have to take advantage of alphabetical listings.
Another tip is to not upgrade a design that is currently in use and override it. Remember to change the name.
If you do this, you avoid an annoying bug where the ships of the current design lose their icon graphic when selected. I prefer to manually upgrade them to a new separate design and obsolete the old design to avoid any trouble.
Anyone notice how the game keeps track of all designed ships even when you obsolete them. You can see this on the quick build menu*. There should be an option to toggle visibility of obsolete designs on or off for that screen and the shipyard. I used to upgrade ships and overwrite the old ones. On the quick build menu it would show about 10 designs with all the same name! It is very annoying.
I'm not sure if deleting designs removes it completely or not. It seems like the quick build menu is showing the contents of some data structure that wasn't cleared properly when the design was obsoleted from the shipyard. I am guessing it's a bug. Another reason to make sure you name your ships well until these bugs are ironed out.
*The quick build menu is the menu you see when you change ship production from the colony screen or from the galactic view on the tool bar, when you click build ship.
Just a couple cents.

When I design a new ship I always make a prototype. This means I make a ship that is only a hull and extras.
When I wish to make a production run ship I "upgrade" the prototype, change the name, and add weapons and engines etc.
This should help avoid an elusive bug involving upgrading ships and being unable to change them or unable to remove certain parts. It also meens no more removing old parts should you choose to upgrade a fully equiped ship.
Also your prototype designs will be visible as soon as you get the hull tech; the best reason to do this!
I also label the ships in a way that is easy to track on the list.
A-NAME-M[x]
The first letter is A-E. Each letter represents a hull type from Huge to tiny. I use U for Constructors and Transports.
The next is simply some fancy name for the ship and the last indicates its Mark.
A-X-NAME
This is the Prototype listing. It obviously forces the prototypes lower down the list.
Until the game has a better way of organizing the ship designs, I have to take advantage of alphabetical listings.
Another tip is to not upgrade a design that is currently in use and override it. Remember to change the name.
If you do this, you avoid an annoying bug where the ships of the current design lose their icon graphic when selected. I prefer to manually upgrade them to a new separate design and obsolete the old design to avoid any trouble.
Anyone notice how the game keeps track of all designed ships even when you obsolete them. You can see this on the quick build menu*. There should be an option to toggle visibility of obsolete designs on or off for that screen and the shipyard. I used to upgrade ships and overwrite the old ones. On the quick build menu it would show about 10 designs with all the same name! It is very annoying.
I'm not sure if deleting designs removes it completely or not. It seems like the quick build menu is showing the contents of some data structure that wasn't cleared properly when the design was obsoleted from the shipyard. I am guessing it's a bug. Another reason to make sure you name your ships well until these bugs are ironed out.
*The quick build menu is the menu you see when you change ship production from the colony screen or from the galactic view on the tool bar, when you click build ship.
Just a couple cents.
That while a AFr-303 would be the third version of an attack frigate.