Are there ways for multiple saves for alternative games?

I have installed an alternative for an installed game I played for years. Additionally, they are the same game so they have the same Save Data Location. Virtually, are there ways that I divide them into two folders which an old one got the Save Data Location whether the new one got the whole new Save Data Location that I can play both of them differently? Could you response the inquire I give?

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

You can set up a portable build for something like this. It would have it’s own save files and config.

To set up a portable build, go to Download Citra - Citra and select Manual download. Then under Nightly Build, click on your operating system’s icon to the right of the latest build available to download the build.
Extract it (7zip can be extracted using Winrar or 7zip) (.tar.gz can be extracted natively on MacOS) and put it where ever you wish. Inside the extracted mingw folder, create a folder called user. This Citra should now store all of its config, save files and such inside of this user folder)
Check to make sure that this user folder is in the same folder that contains citra-qt(.exe)
Now run the citra-qt executable found inside of the mingw folder.