Hi Dan,
Welcome to our community forum!
You can upload a CSV file from Stop & Go to an Emlid Flow project in your coordinate system and vertical datum. Emlid Flow will apply the projection and geoid automatically. You can find more details in this Support tips post.
One important note – the base’s datum in Emlid Studio and the project’s datum in Emlid Flow should match for proper conversion. So, if the projection is based on NAD83, you’ll need to enter base coordinates in NAD83 in Emlid Studio.