Ghost themes show comments through the {{comments}} helper in post.hbs. Put the Crowment embed code there instead.
Sign in to Crowment, create a comment widget for your site's domain and copy its app key from Install & Embed.
In Ghost Admin, go to Settings → Design & branding → Change theme, and download your active theme.
Open post.hbs, find {{comments}} and replace it with the embed code. Keep it inside the {{#post}} block, so {{id}} gives the post's ID and the thread stays attached even if you change the post's URL:
<script defer src="https://embeds.crowment.com/comments.js"></script>
<crow-comments app-key="YOUR_APP_KEY" page-id="{{id}}"></crow-comments>
Zip the theme folder, upload it under Change theme, and activate it.