There are Qt Widgets applications and there are Qt Quick applications. Choose one.
QCustomPlot
lets you create widgets for a Qt Widgets application.
You can not embed a QWidget in a Qt Quick (=QML) application. The only thing you can do to some extend is to embed QML in your Qt Widgets application. In this case your MainWindow
inherits QMainWindow
only and contains a QQuickView
(see http://www.ics.com/blog/combining-qt-widgets-and-qml-qwidgetcreatewindowcontainer).