The Unpaywall dataset is indexed using Crossref DOIs. If the articles in your journal have Crossref DOIs and are available on their landing pages (wherever https://doi.org/YOUR_DOI leads), we'll find them automatically. If we don't, let us know and we'll fix it.
For now, if you don't use Crossref DOIs - or don't use DOIs at all - it's not currently possible to index your journal in Unpaywall. We're planning to work with DOIs from other registration agencies and add indexes based on titles and other metadata, but we're not there yet.