Or is there a way to index both spouses?
We index the most recent spouse. The researcher will see both when they look at the record.
It is always best to include the shared batch code so we can look at the batch to verify we see what we think you are talking about!
Here is some official direction on your question. There may also be something in your project instructions or field help. To share your batch, in the upper left click Batch; Share Batch.