When should I use the Flask.config vs. use flask.session?
Yes, most definitely.
The config is for global, project-level variables: the location of files, keys for any APIs you might be using, your database access settings, things like that.
The session is for variables related to the current user's session on the site: their previous choices on a multi-page form, preferences, login details, etc.
You definitely don't want to get these mixed up.
Is there a rule for when to use Flask.config vs. flask.session to store variables?