The charger will only charge out of the banana plug jacks, it will NOT charge out of the Balance plug jack.
If you can find or make a cable like this, then you can use the NiMH setting on your charger,
Unique cable lets you charge directly through the balance lead with 2S JST-XH batteries
www.progressiverc.com
otherwise you will need the specialty charger that Frsky makes,
PERTH'S DRONE & MULTIROTOR SPECIALIST We have a passion for Multirotors and other flying Machines and hated having to wait for parts from overseas so we started our own hobby store. We have collected some of the best parts from around the world making them available quickly and at a...
buzzfpv.com.au
Even if you send the green NiMH battery back and get some 18650 cells for the battery pack that comes with the radio, you will still need some specialty charger for those, they don't make a "18650 to banana plug" charge cable, so you would not be able to use your existing charger to charge 18650 cells.