Hello there, hannahgracenisse.
I'd like to welcome you first in the QuickBooks Community.
When you let your client pay the invoices online, the actual funds will be deposited to the bank account that's linked to your QuickBooks Payments account. You may log in to your QuickBooks Payments account to see and review your transactions: Search for transactions in the Merchant Service Center.
For it to be recorded into your QuickBooks Self-Employed account, you can either manually download bank transactions or connect your bank account into QuickBooks Self-Employed. Then, you can categorize it after. Here are the articles for your reference:
Post again if you have more questions. I'll be here to assist you!