Else just run the 12V into the Arduino DC in jack, too.
Can i also do it at the Vin input pin of arduino?.. and what's the max current and voltage can be supplied in the Vin?
Yes, as long as it's not the VCC/+5V pin. The main idea is to send it in ahead of the power regulator, not after it :-)
Current is never "pushed" -- the Arduino will draw what it needs. If you try to draw more than about 200 mA THROUGH the Arduino, it may fry the chip. This is why you use buffers and transistors and driver chips on the output when driving strong things like motors.
You need a regulator that can provide at least 5.5A 6V. That's a *lot* of current; most regulators don't do this. You'll probably end up with a "power supply" more than a "regulator."
Although you can get a number of 3A regulators, and use one per motor. However, using linear regulators like that is a big waste of power -- you'll burn off half your battery power in heat before it even gets to the motor. Use a switching power supply instead.
Also, if you are driving the motors with PWM or stepper controllers or similar, you want more voltage available to the controller than the ratings of the motor, and then want to current limit the motors instead. With the right drivers, you can run the 6V motors directly from 12V, without needing a step down at all.
Here's a 5A power converter that can go from 12V to 9V, for $19: http://search.digikey.com/us/en/products/APXW005A0X3-SRZ/555-1172-1-ND/2341120