Branding at top left in a Jamroom skin
Design and Skin Customization
What I did was pull a copy of the default JR logo image from my server, and noted its file size and dimensions and file type. Then I created my own logo that was the same type file and general dimensions, and named it the SAME name (I think it was "logo.png"?). Then I replaced the jr file with my own, on my server, in the same location(s). Then refreshed cache and icons.
My own logo then showed up instead of the JR one, and because nothing else had changed (like especially the image file's name), it still worked as a hotlink to Home page. The key thing here is that the system didn't notice anything had changed.
Later on I played around with making that logo and header taller, etc. You want to keep in mind about mobile devices though, and not force it to be too big.
I guess it's just one way of doing this among various ways. I sort of stumbled into it and it worked.