On my test forum I'm having issues with the logo.
I'm putting the link into the board logo part of the theme but the logo isn't changing.
Don't worry la la land again. I went to the main forum and it shows it. It doesn't change in the admin.
The ACP stays unaffected of any changes. And that’s for the better. We don’t want to have any changes that could accidentally lock us out. 
Today I've pushed up a change to aid theme image management.
From the theme images section, you can now drop files to upload. The images will be added to your file manager for now and then automatically linked in the form input. (You'll need still need to hit save).
Longer term I expect themes to have their own storage unrelated to the general file manager.
Additionally I've added a little toggle to the image preview so that you can see the image on a darker background.
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