The file to edit that allows you to specify which ships you start with is: GalaxyScenarioDef.galaxyScenarioDef
You will need to define the ship if it is a new custom ship in the 'planetItemTypeCount' section, where you give it a 'designName' like: "Vulcan:Frigate:Scout", and the reference to the entity, e.g. entityDefName "FrigateVulcanScout". Make sure you increment the planetItemTypeCount value by 1 if you're adding 1 ship.
You will then need to decide whether you're adding it to Psi, Phase or TEC and locate the appropriate section to add it. You'll find this section if you scroll down in the file to: 'planetItemsTemplate', and for the section: templateName "Template:DefaultHomePlanetSetup", you'll append your new planetItem to the existing list, e.g. item "Vulcan:Frigate:Scout". Also, increment the item count here as well.