I have tried to find this on the forum and since it hasnt seem to come up at all I'm guessing I'm just missing something. One of the galatica damage tokens is just a red silhouette of the ship which is the same way the basestar damage token shows structural damage. I take this to mean that this is structural damage for the galactic also. Here is my question, if that is the case then does that mean that basestars and and raiders now damage the galatica on a 2 or better instead of 4 or better as the base and how do you repair that damage since it is not a location?

I'm pretty sure that I am missing something really obvious at this point but I just can't see it.

Being a total noob myself i asked the same question, when it came up in our game. If its the token i'm thinking of its the exact same symbol next to the fuel "wheel" It is a resource damage token and you subtract one from fuel. (or what ever resource is depicted)

Raz_wolf is correct. Two of the damage tokens don't damage a location on Galactica but instead reduce their corresponding resource by one, and are then removed from the pool of damage tokens so that they can't reduce that resource again.