Depending on how many of these albums that are duplicates in different versions that you have will change how you approach this problem. There are many ways to do it. Let's assume you only have a handful of these; like 12 or less. I'll outline one way of doing it for you.
But first, let me tell you how to change metadata inside of MC. Metadata meaning things like Album, song Name, Artist, etc. To change any of these, highlight the files you want to change. Then open the Tag Action Window with Edit > Tag . On the left, you Tag Action Window will open, showing you the basic tags. You can change which tags show with the little pulldown gear icon on the Tag Action Window.
To change a value, just type! If you want to add "DSD" to the end of the Album tag, just click in the tag, go to the end and type a space and then DSD. Click anywhere else to save. Now those files have a new Album name.
So, how do we separate out files that all appear together, but are part of two different versions of the album? Here's one way:
1. Click on the album in question so that it shows all of the files. Notice that there are two copies of every song.
2. Go to the headers of the columns that show Album, Artist, Name, etc. Find the filename column.
3. Click on the filename column to sort on this field. It will ask you a question. Tell it to temporarily sort by filename.
4. Now you can see the files grouped by filename, which should group files in the same folder together! So now your albums should be grouped together. Now we can select one of the groups and rename the Album.
5. Select the files for the DSD version, or whatever version you want to name differently than just "The Album Name".
6. Open the Tag Action Window as above, edit the Album name, and click somewhere else to save.
7. Now go back to your album list and refresh to see your changes. The Albums should now be separated.
This seems like a lot of steps written out, but you can do it really fast once you get used to it. If you have only a handful, this will work quickly for you. If you have dozens or hundreds, we might need to engineer a different approach for you.
Good luck!
Brian.