I ended up downloading the template, and modified the maptour-config.js and it works fine: http://agsmaps.ci.santa-rosa.ca.us/map_tour_park/ I've only added a few photos as a proof of concept to show to the departments.
So this brings up some more questions. I see using this template multiple times. Do I just copy the folder that I created in wwwroot and then make my changes? Also, how do these sites that I create locally get discovered by Google, etc.
Setting your logo in the hosted version should works. I just tried and it works for me. Did you use a full URL that starts with http:// ? If you still have the issue, please make the tour public and I will take a look.
When using the downloadable, we describe a pattern to avoid copying the application multiple times (update will be painful), in readme.pdf at page 21.
To get search engine referencing, you have to describe your app in index.html using meta tags, open index.html it's documented there. We also recommend to create an item in ArcGIS Online that points to your application, that way you will benefits from arcgis.com reputation.
