My Quickly app requires data files to store settings, configuration and etc. How would I do this inside the app folder. Keep in mind that I will need to read and write to these files while the app is running on a client's computer. Thanks.
This has more to do with general application development than Quickly. Have a look at your home folder and press ctrl+h or the equivalent to show hidden files in your file manager.
Applications who need to store usersettings do this by creating a hidden folder (prefixed with a dot) and write the configuration files there. Other stuff like a database, extra plugins etc can be put here too.
This has to be done in the code at runtime, not during installion. Something like this should be enough: