If you want to read how many amps you are pulling through your system you would have to put the sensor across the two batteries, not just one. Otherwise it would just show you about half the amperage.
When you have two packs in paralell, you have the same voltage, you pull the same current, but you have double the mAh in your tank. So if you want it to show the voltage, you can put it either way. If you want to see the right amount of mAh's that have been used or the right amount of A's that you are currently using, then you need to put it across both batteries.