Welcome to the Community, Brendan.
One of the reasons why the estimate template you created is not being applied when sent to your customer is that it is not set as the default template in QuickBooks Online (QBO).
To set it as the default template, follow these steps:
- Go to the Gear icon.
- Choose Custom form styles.
- Click the dropdown arrow next to the Edit option corresponding to the estimate template you created.
- Select Make default.

If you're using the old estimate layout, you should see a checkmark for the estimate template you created when clicking on Customise, indicating that it will be used as the default template. You may want to click the Print or Preview option to confirm this.
On the other hand, if you're using the new estimate layout, make sure that the estimate template you created is the one being used. To do this, go to Manage, then select the Design section.

Additionally, you may want to review the Online delivery section in the Sales tab under Account and settings to select how you want your sales forms to appear in emails.
Since you're new to QuickBooks, I've added some articles that you may find helpful regarding estimates, whether it involves adding a logo to them or converting them into invoices:
Feel free to leave a message in the Community should you have any other concerns.