I've run my reactor on both the intake and output, and both worked ok. If your reactor has media in it, then I'd put it on the output so it doesn't get gunked up. I actually just run mine right into my canister intake nowadays. As far as killing the bacteria, I don't seem to have issues in my tank, but realistically I have no way of knowing how much or what sort of bacteria is growing in my canister. The muck that accumulates in the filter looks just like every other bacterial slime I've seen.