If I understand properly (not sure), you have two questions.
1) You have added a custom column to CC's grouping drawer, using lookup name #series_or_not. You see this column in the grouping drawer and you can tap on it to see the values in the column. Your issue is that the group is named with the columns lookup name (#series_or_not) instead of the column's display name (Series Or Not).
This is expected behavior, and has always been like this. CC does not use the display names. It doesn't know what they are when the column is added to the grouping drawer, and they can change from library to library.
CC does know the display names in book details because they are part of the metadata for each book.
2) You have a yes/no column #read and have added it to the grouping drawer. You want to know how this differs from the built-in Read column and how to make it work.
See the set of questions & answers in
CC's FAQ "Marking books read and syncing that information with calibre". That group is the fifth bullet point.
Did I understand your questions?