I am making my first Flask app. I tried deploying with FileZilla but FileZilla runs index.html before it runs index.py. Am I suppose to use a different software to host it or should change the way my files are organized?
Any help would be appreciated! Thank you!
Most traditional shared web hosts will not be set up for Python web applications. It can be done (for example, FCGI is an option, or even plain ol' CGI technically) but you would need to talk to your web hosting provider to figure out what tools they offer.
If they do offer FCGI, http://flask.pocoo.org/docs/0.12/deploying/fastcgi/ has some instructions on how to set it up using Flup. It's also possible (but a long shot) that they support mod_wsgi or similar, in which case you could use that.