As far as I know, they do nothing extra under normal circumstances other than consume more electrical power (current A x voltage V.) I've noticed that if you leave the entire system off for a few hours and then kick it back in, values will return to their normal levels faster with both main and backup systems active.
For the most part, it's a good practise to leave them off when they aren't needed, but activate them at critical times such as launch and reentry. Under emergency power, do not use both systems as it will shorten the fuel cell's lifetime drastically. (Of course, AFAIK there is no possibility of APU or generator failure which would necessitate use of the emergency fuel cell...)
