I haven't tried this, but, if you create your own set of ships, and create your own ship style, then select that as your custom race's style, then they should auto-update.

You could just replace a few ships in a default set if you don't want to create an entire new ship style yourself, just save it as under a different name, create your custom race, and enjoy.

*not guaranteed to work, as I never got a custom ship style to work properly with the drengin super ability, I forget it's name. 8)

Have a look to the Ship naming strategies thread and be welcome in the wonderful world of ship designing!

Don't forget to activate ship's design save to HD option as said above, and save a template only for a new ship design, not for a given ship upgrade, unless you add non functionnal components.