Trying to get into this game again and I'm already lost before it's even booted. Help?

Hi, I've got the GOG versions of the base game and Zubmariner expansions but, unusually, the two have completely separate installers and exe files. Do I have to run the game through the Zubmariner exe to get all the content and if so does the original Sunless Sea installation need to be there for it to work? Am I missing stuff from the original game by playing through the Zubmariner release? Do saves transfer between the two or do I have to pick one and stick with it?

Thanks in advance, all.