Not sure if I understand your problem correctly, but anyway:

In the options menu, deselect "save ships to hard drive" - this means the customised designs are no longer stored between games.

When designing a ship, don't place any functional components. Save and check the "Also save to templates" option. You can then use that template for customising in future games.

I have a standard template for each Hull size of ship - and have given them names...
Tiny....Corvette
Small...Sloop
Medium..Frigate
Large...Destroyer
Huge....Cruiser
Cargo...Civilian

After I've added the "Bling", I saved it as "Corvette Template", "Sloop Template", etc.

Regarding naming conventions, I do this. Say I'm attacking with missiles and defending against Beam. I might call a sloop "Sloop Lancer". Now, when I graduate to Frigates (against the same enemy), I would call it "Frigate Lancer", etc. Then, anytime I needed a Missile vs Beam ship I would use the Lancer series.

Another time I might need Missile vs Missile. I might call these ships "Sabre".

After these designs have been created (and saved), I merely select the type of ship that I need for the occasion. The name "Lancer" or "Sabre" remains consistant through all hull sizes.

Additionally, the subject of miniaturization comes into play. Sometimes there need to be variations that I want to keep - depending on my level of miniaturization. I might call these ships "Frigate Lt Sabre" or "Frigate Hvy Sabre".

In the description field (before saving the design) I use something like this...
Att:12, Def:3, Spd:7, Sns:5, Rng:0.2

I have also created spreadsheets that list my designs - 5 or 6 on a page. The information for each design includes...
Name
Miniaturization Requirement
Stats (Cost, Maint, HP, Size, Raw Wt, Log, Speed, Range, & Sensors)
Combat Data (Beam, Missile, M Driver; Shield, Pt Def, Armor)
Components (Hull size, Engines, Sensors, Modules)
Weapons (Cost, Size, Name, Qty)
Defense (Cost, Size, Name, Qty)

Having this data in my "GalCiv Binder" enables me to direct my research towards the technologies that I need to produce a specific type of starship.

Galactic Civilizations has been developed over many years, and is extremely information-heavy. Using spreadsheets helps to get a handle on the "Bull"

Basic idea -> empty the appropriate 'ships' folder in \My Documents\

For DA metaverse empty the following folder:
\My Documents\My Games\GC2DarkAvatar\Metaverse\ships
For DA regular empty:
\My Documents\My Games\GC2DarkAvatar\ships

'My Documents\My Games\GalCiv2' also has 2 ships directories like the ones above which you empty if you're not playing DA.

Good luck!