no, electricity is lazy like me and will always find the shortest route, you would have to put plus on battery 1 and negative on battery 2. If you don`t do this you will get lots of weird and wonderful issues, i see it every day with big banks of batteries installed on boats and ships.
Giles is right. But, on a car the situation is slightly different:
1 - The trickle charge on a car battery is very low, after a while, and the current (both charge and consumed by alarm etc) is close to zero (in practical tems). Therefore the voltage difference between the two is very small. Also, the cable between the two batteries is thick and short, with a very low voltage drop. (rated for starter current) Then add this to the next point:
2 - The batteries are connected in parallel all the time, not only when the charger is connected/charging, and that will even out any differences.
3 - For a car with 24 V start (and 12 V parallel normal), the positive pole on one battery and negative on the other will during start either be at 24 V relative to each other, or at zero V (shortcircuited). Neither of these situations would be very much liked by the charger (although the 24 V into the output might be OK, depending on the construction).
The most important issues for vehicles with two batteries are that the two are equal in construction and age, preferably a matched pair; and that the connection between them are in perfect condition, both terminals and cable. Still, if it is convenient, and you don't have 24 v start (or never start with the charger connected), connect one pole to each.
If you, on the other hand, charge the two batteries with a powerful charger (or booster) out of the car, where the interconnect cables might be smaller as well, there will be a considerable difference in charge level if both charger leads are on one battery.
For stationary batteries, (radio station, emergency lighting, navigational instruments, etc), the charger is actually the power supply most of the time; and there is a constant, high, charge voltage. Any small difference in voltage between the two (ore more) batteries will result in a permanent difference in charge level. This will accumulate over time and be detrimental to the battery's health and longevity.