I want to say that a 50 ft run should be fine with a plain old line level RCA cable, but on the occasions where I have run RCA cables past 35 ft, I have always had problems. However, that also may be because I wasn't able to isolate the cable from power cables. In theory, an unbalanced cable should work for that distance.
I would play it safe for long runs and use balanced cables.
You can use unbalanced RCA for short runs and balanced for long, the processor will not care nor will the subwoofer. You can use different subs for zone 1 and zone 2.