Our webpage is taking 2% deposit through shopify and the rest is being processes through QB. How can I autopopulate an invoice through QB for the first 2%?

You can utilize a connector to reconcile the Shopify transactions and avoid duplication.

https://synder.grsm.io/quickbooks

Thanks for posting here in the QuickBooks support page, @info-trilliumste.

I want to make sure you're able to sync your deposits into QuickBooks Online.

For this, you will need to use a third-party importer app to transfer the deposits from your webpage and into QuickBooks. You can use the link provided by Fiat Lux - ASIA, or you can visit our app store to find the best tool for you.

 Here's how:

1. Click this link to our site: QuickBooks Online Applications
2. Update the country flag on the upper-right section of the page to Canada.
3. Enter the keyword "importer" or the name of the app you want to connect with QuickBooks.

You can also use this link to establish connection between Shopify and QuickBooks: Shopify for QuickBooks Online.

Please post here again if you have other concerns with QuickBooks and Shopify payments. I'll be right here to help you out any time. Have a nice day.