Naphtas take a long time to throw their grenades and have very short range.
I tend to use them in a similar way to how I use javelinmen: pin down the unit you're attacking with spearmen and lob the grenades above them. When possible attack downhill and never attack uphill or your own spearmen will receive most of the impact. Naphtas are also very useful in bridge defense but again, you'll need either to wait for the enemy to cross the bridge and start coming up or to get your naphtas on the bridge, otherwise they'll burn your own troops.

I guess in principle you can also use them to attack a flank but they're very vulnerable so they'd need to be protected by another unit from being flanked themselves.