You are talking about using two separate interfaces, aren’t you? It seems to work ok here, if you switch the interface in the second instance. It’s not going to remember two interfaces. Or are there problems farther along?
You can change the settings folder in Global Preferences, but I don’t think that’s going to help with this, with the multiple instances referring as they do. But if it just means switching the interface in the second instance each time, that doesn’t seem so bad. If I’m understanding correctly the setup you’re describing.