The nitrogen will pressurise the whole system - if the compressor was 100% gas tight between its pistons/vanes/whatever type it is, the gas would just go the other way around the system back through the expansion valve in the evaporator.
That's assuming only one side has been connected up to their manifold - if both sides are connected up and opened then you're pressurising high and low sides from the manifold.
I've got a few bottles of nitrogen and all the kit to test and evacuate my own systems, but unfortunately my high pressure nitrogen regulator needs a few bits to make it usable that I haven't got yet.
I think I've mentioned before, but on a P38, the obvious culprit for leaking badly is the top corner of the condenser where the foam blocks retain water and accelerate corrosion. The second place is the suction (big) pipe on the firewall where its pressed against the foam. When its running the suction line gets cold and sweats. Condensation is soaked up by the firewall foam and slowly pin holes the rear side of the pipe. Problem is, even with UV dye in the oil, its not obvious, as said small amount of dye that makes it out also ends up in the foam. Soapy water around that area while pumped up with nitrogen is the best way to check.