Over voltage on Arduino and Ardumoto I am using Arduino Leonardo and Ardumoto to drive 2 12v motors running at 1.3 amps each.

I purchased a rechargeable battery of 12V with 5AH

I first started by plugging in the battery to the Arduino via the barrel jack. Arduino then sparks and is fried.

I read somewhere that I wasn't supposed to hook it up to the Arduino and to hook it up to the VIN ports in the Ardumoto. I purchased a new Arduino and plugged in the Positive and negative from the battery to the ports and now the Ardumoto board fried (copper lining on board burnt off).

I'm reading online and from what I've gathered, the Ardumoto can handle a max of 18 volts and a maximum of 2 amps per each output. I'm obviously missing something and would not like to fry my boards next time.

Please assist?
From your description, everything should be wired correctly. It should not have failed.

Unfortunately, testing this sort of thing with a 5 amp-hour lead-acid battery is not a great way to get started, since a battery that large can source a lot of current, and doing anything wrong will likely produce immediate and spectacular failure.

Really, the only think I can think of is that you have the polarity of the output lugs/pins on the battery backwards. Buy a $5 multimeter, and check them.