Ikram101:
You can use a current-limiting resistor from the positive end of the battery and connect it on to the Vin pin and complete the circuit attaching it to ground. Btw, how big spikes are you talking about?
There are three motors wired up to the system, so about 85 amps total, with 55 amps on one path. The arduino would be in parallel, but it still worries me.
What size resistor would you recommend?