I always keep the phone plugged into the charger at work all day. Will that harm the batter in the long run
I shouldn't worry about it. The batteries in these phones have an auto shut off to prevent them from being over-charged.
The worst thing you can do is let the battery completely drop to zero.
I thought it was recommended to do this once a month and not more (or once in a while). I ran it down to 0 only once during the 1st few days after purchase after it was charged to 100% (left it an additional hour passed 100% to fully charge), I only did this to calibrate the battery and don't intend on running it to 0, not for a while at least. Is this OK or did I do harm to my new iPhone 6S Plus?
There's no harm to your battery at this stage. However, I wouldn't make it a habit. Completely draining your battery decreases the longevity of it. Charging normally going forward is all you need to do.
I usually put mine on the charger when I get the first alert at 20%. I charge it to about 85%.
It doesn't hurt to drain the battery once in a while but don't make it a habit. Maybe like once very 2-3 month. Or if you all of the sudden notice the % indicator went down a bit and the next thing you now the % went back up. Then you may need to recalibrate the readings.
Since I've gotten my iPhone 6, I've been hesitant to leave it charging overnight. Recently, I've been using BatteryLife to monitor my battery's health and it reported that my battery currently holds 86% of it's original capacity. This leads me to believe that the my charging habits haven't exactly improved my battery's lifespan, if after a little over a year it's health has dropped 14%. For the record, it has gone through approximately 350 charge cycles to this point. I now use a battery case and it is one of the best decisions I have made.