If you were to add to a raid, you need to add a similar template to the gameplay.entity

pirateRaidComposition:4
            requiredShipCount 2
            requiredShip
                type "CAPITALSHIP_PIRATEBATTLESHIP"
                minCount 1
                maxCount 1
            requiredShip
                type "CAPITALSHIP_PIRATECARRIER"
                minCount 1
                maxCount 1
            randomShipCount 5
            randomShip
                type "FrigatePirateMedium"
                weight 6
            randomShip
                type "FrigatePirateHeavy"
                weight 7
            randomShip
                type "FrigatePirateAntiFighter"
                weight 3
            randomShip
                type "CAPITALSHIP_PIRATESUPPORT"
                weight 1
            randomShip
                type "CAPITALSHIP_PIRATESIEGE"
                weight 1

as for the base:

item "Pirate:CapitalShip:Battleship" -> would add the Capital_piratebattleship.entity

in the galaxyscenariodef file under

planetItemsTemplate
    templateName "Template:PirateBase"
(use the find feature to search for it), look until you see the section that list the ships

The game keeps giving me undefined entity ref if I add anything to the galaxyscenariodef file, I decided to add one extra guass defense (and updated the count) to the pirate base to make sure, the game just gives me that undefined error through the dev exe and on load, the extra gauss defense gun that I added isnt there.

Also if I make a new entity, the game just crashes on start saying it can't find a ref even though I added it to the player and entity manifest, why isn't this working for me when it does for everyone else? what could I possibly be doing wrong?

Edited, because i'm not crashing when adding anymore, i'm now only crashing when trying to make new things.

Nope, i've tried doing the most basic things now such as making a mod with unmodded entity manifest, an unmodded galaxyscenariodef in the gameinfo folder and a new entity named "capitalship_techtestbattleship", I then added that new entity to the entity manifest and the test battleship to the "normal start" of tech in the galaxyscenariodef file but the game will just crash when loading the mod again.

No sure if there is a mech for that, probably the only way is to increase the number of supplies used.

  Mooster,   Thank you for the wonderful detail on adding Caps to the game file.    I hadn't tried it, but it looks wonderful!!! 

-Teal

You have to make sure your new ship entity is defined in "Player Pirates".  As well as defined in "gameplay entity". If you added a new ship entity file the game wont see it untill you add it to the factions player entity file.