Ouch! Yes, by all means what was meant was sub black to amp chassis, not vice versa. Keep in mind that with a fully balanced amp, both the red output and the black output of the amp have signals on them (in fact, the same signal except with opposite polarity, as you now appear to realize). When you connected both of the amp's black outputs to sub chassis, you were connecting two different amp output signals together, a definite no no!
I don't quite follow the two alternatives you listed at the end of your post, but let me re-state how I envision the connections should be made:
-- Left main speaker red to Ayre left channel red.
-- Left main speaker black to Ayre left channel black.
-- Right main speaker red to Ayre right channel red.
-- Right main speaker black to Ayre right channel black.
-- Sub left channel red to Ayre left channel red.
-- Sub right channel red to Ayre right channel red.
-- One or both of the two black terminals on the sub to the chassis of the Ayre. I suspect that it won't make any difference whether you connect both of them, or only one of them, since they are most probably connected directly together within the sub's amp.
Regards,
-- Al