Currently, if you want to assign a snapshot store to a certain project, it is required to access the Admin view and configure the "Assignment Labels" property under Backup > Snapshot Storage with the name of the corresponding project.

AFAIK, it is not possible to assign this configuration in the Ops Manager's YAML. E.g.:

s3Stores:
- mongodbResourceRef:
    name: s3-metadata-db
  mongodbUserRef:
    name: s3-meta-store-user
  name: s3store1
  pathStyleAccessEnabled: false
  s3BucketEndpoint: endpoint1.corp
  s3BucketName: backup1-bucket
  s3SecretRef:
    name: s3-credentials
- mongodbResourceRef:
    name: s3-metadata-db
  mongodbUserRef:
    name: s3-meta-store-user
  name: s3store2
  pathStyleAccessEnabled: false
  s3BucketEndpoint: backup2.corp
  s3BucketName: backup2-bucket
  s3SecretRef:
    name: second-credentials