When you say "doesn't show up in their account" do you mean that you took a payment from a customer and it isn't posted against any work so your customer should have a credit?
If so, AND you entered it as a deposit, it all depends what the offsetting account is.
If you want to use the Bank Deposit screen, then you need to select Accounts Receivable as offsetting account and make sure you mark the payee as the customer you got it from.
The other option is instead of Bank Deposit, use the Receive Payment task and select the customer. This will automatically create a credit for your customer that you can apply to future invoices.