The simplest solution is to setup a merchant account and just log the wire transfer every 3 days from there. Balance this account with a lump sum sales receipt and a purchase invoice for the charges.
Handling bulk payments from merchant accounts
If you’re using Zapier you can also auto-import your sales from Shopify.
https://zapier.com/zapbook/zaps/6900/create-quickfile-invoices-from-shopify-orders/