The app ships via FBA the Shopify SKUs that have a matching SKU on Amazon FBA. When the SKUs on Shopify and Amazon do not match the app does not ship via FBA automatically.
If you have different SKUs on Shopify and Amazon then you can use the SKU mapping service to link the different SKUs so that the app can ship via FBA even if the SKUs don't match.
Consider, you have an item with SKU SH-SHOE-55 on Shopify. The same item has the SKU AM-SHOE-55 on Amazon FBA US. To link the 2 SKUs go to Shipr dashboard > Settings > SKU Map page and save the 2 SKUs. Check the image below:
When SKU SH-SHOE-55 is ordered on Shopify, the app will attempt to ship AM-SHOE-55 via Amazon FBA.
You can map different SKUs for each Amazon FBA region.