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Hello there, @TBW1,
The program is a cloud-based system and we value data security thus it requires your customer to click many links to open the full invoice. This is only happening when using QuickBooks Self-Employed (QBSE) on the phone.
If you're using QBSE on the browser, the full invoice will automatically pops-up when your customer clicks View Invoice. Please see the screenshot below to serve as your visual guide.
Please know that I'm listening to your comments about the sub-heading of "QB Self-Employed Welcome Email" when your customer received the invoice email. There's no currently an option to change the sub-heading name.
If you need to mark the invoice as paid even it hasn't been sent from the account, it's currently unavailable. Yes, you're correct in downloading it as a PDF and directly email it to the customer as an alternative.
Since you want a better functionality, you might want to check the features and prices of our online versions through this link: Compare Self-Employed and Online Versions.
If you find the online version greater benefits, you can watch these instructional videos to help you get started through this link: Getting Started.
This will help improve your experience not to give up QuickBooks, @TBW1. If you need anything else, please drop a comment below. I'm always here to help.