Will disabling the app reset my settings to default values?
No, disabling the app (which can be done at any time from the app preferences page) will not reset the configuration settings.
When you disable and re-enable it, you will find the same custom settings which you have configured for your store.
For your convenience, even if you uninstall the app, the configuration is stored for a couple of months. Consequently, if you uninstall the app and re-install it again in a few days, the configuration will be preserved.