Ah! Thanks for that clarification. Unfortunately, there's not currently a way to add a logo on top of a cover image directly in Rise 360. That said, depending on the cover image you chose in Content Library 360, you may have a workaround.
When you're browsing Content Library 360 photos, putting your cursor over a photo may give you additional attribution about the photographer and the external image library the photo is from. For instance, if the attribution says it's from Unsplash, you can also track down that image on Unsplash.com and download a copy for free there. Once you have that, you can then use photo editing software (or even PowerPoint) to combine the image and your company logo. Then upload it to your course as a new cover photo.
So it's a few more steps to include a photo and your logo together in your cover image, but it should give you the results you're looking for.