How can I customize these games to reflect my company brand?

There is a wide range of customization options:

Modify an Existing Template
Choose a template that you like and then modify the design of the question pages, feedback and results as much as you like. The color palette, fonts, and graphics can all be completely customized. Some knowledge of CSS would be very useful.

Add Your Brand
Add your company/product logo to replace the default H5Engine logo. You can also simply remove the H5Engine Logo.

DIY (Design It Yourself)
Create and upload your own title screen and then modify everything else for a final game that is completely yours.