Hi JustOz,
Thanks for posting your concern in the forum.
I understand you are just trying to find the best way to record your Shopify payments. In my understanding, how you record your Shopify payments will depend on your preferences. But if you already recorded the Shopify payments in a clearing account, you could do a Transfer Money transaction to move the Shopify payments from the clearing account to the correct bank account in the ledger. Also, I would suggest following what other users who use Shopify did to record their payments.
Let us know if you require any further assistance with this.
Thanks,
Genreve