Thank you for reaching out, @Rachael.
Shopify and QuickBooks Online (QBO) have different inventory tracking systems. In QBO, the inventory will only deduct if you directly invoice the customer. However, Shopify has a different tracking system for e-commerce, which is not directly adjusted to the QBO inventory. The reason why the two systems have different inventory tracking.
- Create personalized invoices quickly by adding your logo and colors to a template.
- Use QuickBooks Time and Google Calendar to add billable hours to your invoices easily.
- Get real-time tracking.
Furthermore, you can explore third-party apps to provide more convenient and efficient solutions for your company's needs, as @4Gal suggested.
Regarding your second concern about sales sitting in a clearing account and the appropriate accounting and procedures for moving them out, it's recommended that you seek the advice of a professional accountant. Consulting with an accountant will help ensure records are accurate and error-free.
I hope this helps! Feel free to stop by if you have more questions. Keep Safe!