The message to customer on my invoices is the same over all my templates, but i want a different message on my deposit invoice.

Hi Jack Slater, 

You're correct, the Message on the invoice field is the same across all templates. You'll want to manually add the message every time you create an invoice or use the Footer section to enter the deposit terms. Let me show you how: 

1. Go to the Gear icon and click Custom form styles. 
2. Look for the normal invoice template or deposit invoice template. 
3. Click the Content tab and select the Footer section of the template.
4. Enter in the Add footer text field the message you'll want to add.
5. You can look at the sample template on the right where the information is displayed. 
6. Click Done.

Feel free to look into this article on how to customize invoices, estimates, and sales receipts in QuickBooks Online.

Just leave a reply below if there's anything else that you need help with. Take care and have a good one!