I am not sure how to set it up in 1.2.0, but let me try to shed some light on 1.1.7. First you must be in expert mode before turning this one.
Print Settings > Output Options > Complete Individual Objects > Check!
As you mentioned, you are going to want to set your clearances for your objects in both they XY plane, and the Z direction.
If you would like to print multiple groups (print three of this item, move to another location and print three of this item) You will want to combine your multiple STL files into one STL file. The number of parts you can print in one group, will be defined by layer separation. The longer your part has to cool before having the next layer put down, the more layer separation issues you may run into.
If anyone has some insight into getting this done with 1.2.0 we would love to hear it.