Hey Eli,
First, congratulations on completing your first full length record.
Each version should have a different name with your PRO (BMI) and only needs one name with the copyright office.
For PROs (I’m with BMI) register the original title (ie: “A Great Song”) and then add alternate titles (ie: “A Great Song Instrumental”). This way, when either title shows up on a cue sheet, you’ll get your money.
When using copyright form SR (sound recording) you can copyright the underlying aspects of your songs: composition, performance, arrangement, sound recording of your CD. So that essentially would cover you for any version of that one title (alternate mixes; cut-down versions and instrumental beds). You’ll see this under “Author Created” on the copyright form online.
Paul