Thanks for reaching out here in the Community, @thelittleguy. I've got you covered, and I'll ensure you can get through this so you can download your invoice and show your company logo on it.
A possible reason your company logo wasn't included when you downloaded your invoices is that, the Use letterhead paper button's been ticked from your custom form style setting. Know that if you've checked the box for Use letterhead paper in your invoice template, it takes away your company logo from the template.
To verify if this is the case, you'll want to check the custom form style you're using on your invoices. I'll gladly input the steps below. To begin, here's how:
Access your QuickBooks Online company.
On the upper-right corner, click the Gear icon.
Select Custom form styles under Your Company column.
Choose the template you're currently using on your sales forms, and then click Edit.
In the Design section, click Edit print settings.
If the box beside the Use letterhead paper is ticked, uncheck it so your company logo will be included when you download your sales forms.
You can click the Preview PDF to check your invoice template.
You can also check this article about customising a report in QBO so you can run a report that shows you the status of your invoices: Customise reports in QuickBooks Online.
@thelittleguy, If you need further assistance managing your invoices in QuickBooks, know that you can always get back to me anytime. Also, I'll be happy to help you once again if you have any additional QuickBooks-related concerns. Helping you resolve your queries is my joy. Thanks for choosing QuickBooks. Take care, and have a good one!
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