BTW when interfacing to a high voltage chip its a wise precaution to
add 4k7 resistors in series with each control signal, then if the power chip
fries its much less likely to damage the Arduino.
You did common the grounds?
You did add copious decoupling on the supplies to the chip? This is
essential.
the atmega chip on the arduino is heating up like crazy!
Hmm, that should not have happened, and is bad news. How have you connected
the various supplies to the Mega? It sounds like you've over voltaged the
board or over-currented the Arduino output pins and sent the chip into
latch-up (disconnect power IMMEDIATELY if this happens).
A photo or diagram of how everything is connected is worth a 1000 words.