Groups : entities that share the same group in your inventory (car, hand, main inventory, but NOT quickbar) will be added together when dividing up ammo. This is done so that if you place every item of the group they will all get roughly the same amount of items filled.
Limits: This is the maximum amount of items to autofill into the machine.
With Groups and Limits on if you have 10 turrets, and 100 magazines each turret will get 10 magazines, if you have 200 magazines each turret will still only get 10 because limits
With Groups on and limits off each turret will still get 10 because division :), if you have 200 magazines then each turret will get 20
With Groups off, if you have turret-a and turret-b that both use the same type of ammo only the turrets of the type you are placing will be used.
Since I am not at my desktop I can't go into details on how the remote.calls work for setting up personal sets to adjust the limits/groups but there are examples all over.
The next "major" version depending on time will be a lot easier for adding items/groups through a gui type interface. Not sure if I will have this done before .15 though just depends on how much free time I have.