Hello, loganwrapitupkc.
I'll show you a way on how you can instruct your customer to pay 50% on an invoice.
You can add the instructions on the email before sending the invoice to your customer. For a brief explanation on how the customer can pay 50% on an invoice, they'll be given the option to edit the amount.
They can simply click the Edit link on the "Pay invoice" screen. This is what it looks like in their end:

That said, here's how you can relay the instructions to them:
- After creating an invoice, click the Save and send button.
- Under the Send email section, enter the instructions in the Body text box.
- Review the details of the invoice.
- Once done, click Send and close.


You can also make this as a permanent template for your emails:
- Click the gear icon, then choose Account and settings.
- Go to the Sales tab.
- Expand the Messages section.
- Enter the instructions in the Email messages box.
- Click Save then Done.

If you need help recording your customer's payments, please check the steps from this article: Record invoice payments in QuickBooks Online.
Want to know how much you've earned from your sales? You can pull up a variety of reports such as the Profit and Loss report. Check out the articles here for a guide on how to run them.
I'll address other concerns you might have for QuickBooks Online. Just let me know the details down below. Take care out there.