In order to make a custom style for your own use, where all (or some) of the core ships are replaced:
1.
During a game, design enough templates to make up the new style. You'll need at least
one template of each hull size if you want it to be useable by the AIs. If you won't ever use it for an AI race and
don't build core ships, you'll really only need a Cargo (preferably two) and a Medium template to
cover the colony, miner, and survey ships you start with.
2. In AI race customization screen at game creation, pick the style you used when you made your templates, edit it, and save it under a new name.
3. Go to My Documents\My Games\GC2DarkAvatar\ShipStyles and open your style's xml file in a text editor.
4.
Change the <Prefix> value to something unique, with no spaces or
special symbols. Check through the file for any instances of the
original style name you copied yours from and change them to your new
name.
5. Go to My Documents\My
Games\GC2DarkAvatar\ShipTemplates, and rename the .shipcfg files for
the templates you made in step 1 to match the prefix value you set in
step 4.
6. Once renamed, copy at least the three starting ships' templates to GalCiv2\DarkAvatar\Data\ShipCfg as well (this is necessary to make them appear when you use the style for your own race), and rename them to match their roles in the same format as all the other files in that folder. So
prefix_ColonyShip.shipcfg,
prefix_SurveyShip.shipcfg,
prefix_SpaceMiner.shipcfg, etc.
7.
Start up the game, and go edit the style via AI race setup. Pick each
item on the left and double-click the template on the right to assign
it, then save.
Your style should now be ready for use. Whether you use it yourself or for an opponent, the three starting ships (and any future core ships or AI designs if you replaced more) should use the templates you made yourself.