Yes - you can and should register multiple versions of the same song.
If an instrumental version of a song is placed in a film, television show, or ad, you should enter the recording’s details (including new ISRC information) under the original song in your account. The same rule applies to a remix.
If you’d like the splits to be different from the original version, you should register the instrumental as an entirely new song within your account. An example would be when one writer worked on the music and another writer worked on the lyrics of the original song, but you only want to credit the former in the instrumental version. By registering the instrumental separately, you can give the creator of the music 100% ownership of the new version.
Below is where you can add additional recordings to the same song within your account:
Interested in learning more? Check out our blog post: Seven Mistakes to Avoid When Registering Songs.
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