The Logo section has fewer features than the standard Image section, this is because it is designed to work with your Brand Set up and automatically remember the logo image you upload and uses this every time you create a new App.
You can add a link to a Logo image and also adjust the size proportionally by clicking the settings cog or the Logo section in the Visual Designer .
To change the 'logo' for individual Apps just upload the new jpeg image you want to use and then add the link you wish to use for that particular App and it will only apply to that App. To permanently change your logo for future apps click on Quick Setup.
If you want to always have a link for your logo section simply create an App with allthe sections and customisation you want to use for future apps and click on save as template and choose Save as Default Template. You have now updated you default template so every time you create a new App it will now have your new 'logo' with the link you added. To test it simply click on create App and save a new App - it should now look just like the one you customized.