Here you will find the different configuration settings as well as a troubleshooting section. Different tabs address different modules of the app.
Most of the settings are global meaning that all your boxes will be affected. One exception is the General - Task section in which you save custom box configuration.
In general, technically speaking, you will find all the fields which sync to Jira here.
The most important sections are listed below:
You will find guidance on how to get started in this article: Quick start with BigPicture