Your installation is unique , because modern day air conditioners have a feature called reverse cycle , which the compressor can reverse the stages of operation between the high and low side , which allows either cooling or heating stages depending on the expansion or compression of refrigerant.
Normally when you have multi zones , you have a single compressor (large) outside that does the work compressing gas and sends cold/hot gas to an evaporator unit (big coil inside your roof with the fan) .Air runs over this coil and you get a cooling/heating effect, from the refrigerant expanding/cooling.This air is spread amongst your ducts installed in your ceiling. When you add zones this is basically a partition for the air travelling to your outlets(a valve opens and closes and that feeds the central set of ducts .
Think of it as a splitting of a tree , the main feed of air is the central trunk , the group of sub branches from the trunk is the zones , and your outlets are the smaller leaves attached to the sub branch.
Now it is normally not a concern for running two zones off a single compressor , if the unit is undersized it just means it will not cool as effectively(thermal capacity of compressor).
What is more strange is that you have two compressors for a different stage of operation, given what i have mentioned above about the reverse cycle.
Have you check the model number of your unit and seen the specifications for it? for more clarification on its operation.