QuickBooks accumulates the transactions you processed for the whole day. At 3 PM PT, the day's collection of transactions or batch processes into a deposit that you'll find in your account the next business day.
However, deposits from credit card payments will be in your account the next business day. Bank transfer (ACH) payment deposits can take 2-7 business days in QuickBooks.
I recommend contacting the Merchant Service Center to show the deposit status as "Pending". When your deposit is cleared, the status changes to "Funded".