There is only one GC2.XML file, which is located in the GalCiv2\XML folder. And that one you will probably never change.
There are two each of GC2Types.XML and GC2Ships.XML, one each located in C:\Program Files\Stardock\TotalGaming\GalCiv2\Data\English and in C:\Program Files\Stardock\TotalGaming\GalCiv2\MetaverseData\English.
The ones in the MetaverseData folder you also should not modify. Those have to stay consistant for the online games.
The files in \Data\English are the ones that youy can play around with, and they include:
GC2_Conversations.xml
GC2_Hints.xml
GC2Ships.xml
GC2Types.xml
And there are other .XML files in Data\English you can mess with too, that deal with races and planets and anomolies and abilities, etc.
The .XML files are text files, and can be edited in any text editor. I like Wordpad for this job.
The modding guide is found elsewhere on this site, here:
https://www.galciv2.com/Databanks.aspx
And you contradict yourself by saying that you don't want to replace ships by messing around with the game files too much, and then asking how to do just that. lol
Just make sure you back up the original files before you change them, so you can easily recover from any mistakes.