Steam saves your subscribed mods to C:\Program Files\Steam\steamapps\workshop\content\... which you'll have to find the contents.pak file and unpack it using the guide I linked to in the description. When you unpack the mod, you'll find the files that make up the mod including an instructions.txt on how to change colors. At this point, you'll just need to change the image files around to get the color desired, then repack the mod and place it in your Starbound mods folder.

If you can't find the contents.pak for this mod, you can alternatively download the Starbound forum version I posted (also linked in the description) and unpack the AdvancedFrigate.pak