I'm glad to see your post here in the Community. I can share some insights about the depositing process of QuickBooks Online Payments.
Generally, credit card payments take 1-2 business days while bank transfer (ACH) payments can take 2-7 business days. Your deposit cutoff time is 3 pm PT. Payments processed after 3 pm PT go into the next deposit.
You also have to take consideration of weekends and holidays. Please refer to this article for more details: Deposits FAQ.
On the other hand, let me walk you through the steps in enabling alerts for a paid invoice: