Q: How do I resolve this issue of duplicate submission - with the first journal or the second?

This is an unfortunate situation, as you can yourself understand. However, let’s not dwell too much on this, and see what you need to do.

Now, you haven’t mentioned why exactly you did not complete the submission process with journal A. Was there a technical issue? Was your manuscript not complete in some respect? Were you unclear about some guideline?

Also, I assume the journal that identified it as a duplicate submission was B. So, now, you won’t be able to submit to B, unless they will allow you to first resolve the matter with A. If so, what you need to do is write to the editor of A, explain the situation to them, and request their advice on this. You could add that this was an oversight or lapse in understanding on your part and are sorry about this. If they trust your explanation, they may allow you to resubmit. If not, you could submit to B or perhaps a new journal C. Note that for C, you will have to explain the entire situation (with both journals) in detail.

In a worst case, if no journal is willing to accept the manuscript, you may have to leave it at uploading on a preprints repository, so that at least some record of your research is present online. In that case, you can treat this as a learning experience, ensuring that you don’t land up in the same situation again. A lapse once is excusable, but a second time may go against your academic credentials.

As the initial issue seems to be submission-related, you may find it worthwhile going through the following resources:

• What are the first things journal editors look at in a submission package?
• What makes a great submission package? [Video]
• Learn about final checks and revisions before manuscript submission [Course]

All the best for whatever’s next.