Running two libraries is a possibility, but I would suggest a virtual library instead. Once you get the hang of them, they're easier to manage and you're able to search everything.
If you're only using CBR and CBZ files, the search query would look something like this:
Code:
formats:"=CBR" or formats:"=CBZ"
If you're using other formats, you can also use other fields in your search query, such as tags and the aforementioned custom columns.
