Sagepay - Sage50

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Hi, we are currently moving over from WooCommerce to Shopify.  We use Sage50 as our main stock and accounting system.  Payments go through to SagePay and we download the receipts into Sage50, this creates an invoice with the SKU information and prices.  However, with Shopify the information doesn't fully transfer, and comes through as an S2 with no individual SKU information, and on SagePay it shows the basket as empty.

I don't know how to resolve this, and SagePay have assured me that this is possible and works with Shopify, it is just getting the basket to work correctly that I am struggling with.  They have sent me API information but I don't know where to use this information. 

The link below details what should be done for the API:

Can anyone help?