How can I apply time against an invoice without having the customer see the time billed?

Thanks for bringing this up in the Community, Jenny.

When you add a bill or timesheet entry to your invoice, it doesn't remove the entry directly. Otherwise, you can customize the invoice layout and hide the Product/service and Quantity columns so only the amount will be displayed.
 

Here's how:

1. On the upper right side click the Gear icon.

2. Choose Custom form Styles

3. Select the  template you want to edit.

4. Go to the Content tab.

5. And click the Body Section.

6. Uncheck the box for Product/Service and Quantity.

7. Hit Done.

After editing the template, just make sure to set it as default template.
 

1. On the Custom form style, Select the arrow dropdown beside Edit section.

2. Make sure to select Make as default.

Moreover, you may check this article for future reference on how to email or print multiple invoices: Email or print multiple sales form in QuickBooks Online.
 

If you have further question regarding invoice, please don't hesitate to leave a reply message to this post. Have a good one!

How do I add time to an invoice that has already been created and/or paid?

Hello there, @Jenny.

Allow me to guide you on how you can add time to an invoice that has already been created or paid in QuickBooks Online (QBO). 

First off, it's important for you to create billable time entry for the specific customer. Then apply the time entry created to track the billable hours.

Next, you may follow the guide below:
 

1. Open existing or paid invoice with the specific customer.
2. Link the billable time entry from right side icon bar.
3. Once linked, invoice will reflect as partially paid.

I've included visual steps for your reference. 

Moreover, if you want to learn more about how to run reports in QBO, you may check this article: Run reports in QuickBooks Online

We're dedicated to ensuring your satisfaction. If there's anything more you'd like to bring up about adding time on your customer's invoice or any other QBO concern, please do so by leaving a comment below. I'm here to help you. Have a good one!