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 B07N7MGX9T on Shopify. The same item has the SKU 2Y-QSSP-V4H0 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 B07N7MGX9T is ordered on Shopify, the app will attempt to ship 2Y-QSSP-V4H0 via Amazon FBA.
You can map different SKUs for each Amazon FBA region.