Polarity not all that critical when taking a voltage reading. You're just going to get a positive or negative in front of the number you're really interested in. Unless you're doing something polarity critical, who cares?
My bike lives in a garage/work shop. The only time the battery is removed is when doing something like changing a controller or other major electrical work. Point being, many (most?) displays have a pretty good voltmeter built in. That's all I ever use.
I like to charge at 47-48 volts as well. There's not a lot left in them at that point, and common thinking has it that's good for the battery. I would mention though, that most controllers have a low voltage cut off built in to them (LVC), and that value is something closer to 3.0 volts per cell (40v total). That's the drop dead, don't let it get any lower than that because you're going to damage it value. Nice, because the controller's not going to let you....it's going too shut you down!
