Hi there, @kaneika.
Thanks for visiting the Community today. I want to make sure you're able to link the invoice to the deposit you've made through a funds transfer.
It seems to me that you have two different companies in QuickBooks Online. Since you're moving funds from one account to the other, you'll need to record a two-sided transaction by creating a Check or Expense to record the fund transfers out of one business, then receive the funds into the other business. Here's how:
To transfer funds to the other company
After that, log in to QuickBooks Online (Company B). Then, make a bank deposit to receive the fund transfer from the other company. Here's how:
If you're unsure what specific accounts to use, I'd recommend consulting an accountant.
Once completed, apply the deposit entry as an invoice payment. Here's how:
For future reference, here's an article that can help you learn about how to match and categorize the fund transfer you've made from the other company (Company A) to the transactions from your bank feeds.
Feel free to message again if you need more assistance. We're always delighted to help.