actually the charge should be almost the same.
even when the vehicle is not running, the battery's will move power back and forth untill their pretty much at the same level.
only downside to running parallel, when one batt goes, 9 times out of 10 you will need 2 new ones. if you replace one, it will dis-charge or damage itself trying to equalize the power in the older battery. one of the reasons i went with marine batts (plus lots of connectors to hook all your electrical junk too...
)