Hi @remogul320. I'll share information about your invoice.
In QuickBooks Online, invoices and deposits are both money-in or income transactions. You don't have to remove the deposit, just make sure to select your Accounts Receivable account and the project name in each line item to link both entries.
However, I still recommend contacting your accountant for guidance in recording the payment for the split invoice. If you haven't yet, here's a link to use so you can find some to work with: QuickBooks Certified ProAdvisor.
When your clients have outstanding balances, you can create and send them a document showing a detailed reminder of what's coming in due. Use this link for the steps: How to Send Statements to Show Customers Sales Activity?
Let me know in the comments below using the Reply button if you've got questions other than working with payments and deposits. I'll be here ready to lead a helping hand. Take care always!
