Hello,
The 12V port should indeed be wired to the 5A 12V socket on the megatronics, but the capacitor should not explode. There is several ways a capacitor can explode. First it can receive reverse polarity. Make absolutely sure you a: wire the 12V the right way around and b: solder the capacitor the right way around. Another is over voltage, but at it’s current location, it should only receive 12V. However, close by on the circuit, it is boosted to 20V, so maybe I did wrong and you need a 25V capacitor. I always had 25V capacitors on mine. Maybe it is bad caps, but if you already blew up 2, this seems unlikely.
If you try with a bigger cap and it doesn’t explode, please tell me, then I will fix the site immediately. Else send pictures (either through the forum or mail) and I will work from that.
Yvo