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Running more than one driver on the same JTAG UART will cause problems (for example the wrong CPU might clear an interrupt without sending data).
If you're running the basic HAL (it looks like you are) then the easiest way to fix this is to connect each UART only to the CPU you want to use it with - that will prevent the other CPU from interfering with the JTAG UART hardware.
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I don't understand. I have two SOPCs (with their own JTAG UART, NIOS II + C app running on them) - I assumed them to be completely separate (they're generated separately and even instantiated about three entity levels apart from each other). Are you saying Quartus connects their buses together?
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