When changing oil on my softail springer, it looks like the drain plug
drains only the oil in the oil tank, not any oil beneath it in the engine.
Is that really what's happening? And if that's the case, how much old
oil is left in the bike after the change. Most bikes I've had, the drain
plug is in the crankcase at it's lowest point.

 

Answer to your first question, Yes
About a quart
Refill will 2.5 qts with filter change
This is assuming you have a "twinkie"

 

Perfect, thanks.

 

If you want to get all of the old oil out you can use one of these...
http://roguechopper.com/

 

Your bike has what is known as a 'dry sump', as do all Harleys since the dawn of time (and many other brands). There is no oil stored in the crankcase, it is drawn from the oil tank and returned to it. After you replace the oil filter and have drained the tank I doubt if there is any more than half a cup left, in the oil pipes between tank and engine, oilways around the engine, plus small amounts trapped in nooks and crannies around the engine.

 

Interesting. I just looked it up. So my 88B takes 2 1/2 quarts after oil and filter change.
The book says 3 1/2 quarts (it's a Clymer, so I take it with a grain of salt). So where's the other quart?