Hi Frank.
Where to put the Shortlist template?
You can totally put the Shortlist application from the zip file onto the website where you have your portfolio. The downloadable story map templates, like the Shortlist, are just a bunch of files pretty much like any other so stick them into a folder on that website and you'll be good.
Where to put the photos that the features in your Shortlist will reference?
Your features can reference images at any URL but the easiest thing is to put them into a folder on your website. It can be any folder and doesn't have to be the same folder that the Shortlist template is installed in.
Where to put the CSV files defining the features in your Shortlist tabs?
You upload these CSV files into the ArcGIS Online web map that your Shortlist will display. Create a new web map in ArcGIS Online, open it up, and then in the web map choose Add > Add Layer from File and browse to your CSV file(s). So your CSV files are uploaded into the web map. The web map and all the data it contains is stored for you automatically in the ArcGIS cloud.
The final step is to edit the line in the config section of the Index.html file in your Shortlist installation to point at the ID of your web map.
Rupert