Sorry for the confusion, when I talked about polarity I was talking about it in reference to directionality which is a function of a polarizing potential transformer or current transformer. The polarity of the current transformers is not important as long as they are all in the same direction. When using directional relays the polarity of the current transformers is extremely important. As far as whether the current transfromers are on the bus or feeder side is not important, they will function the same either way.
The system you describe may be a matter of physical space rather then relay protection. It would help if you could supply the wiring for the current transformers and the 50/51 relays.