Are you sure it's low? Did you have it tested? As sd said if its low you have a leak and you'll just be recharging again in a short time.
As far as what one to charge from, I'm not sure I've never done it myself as I don't mess with refrigerant. I'd venture to guess the low side, as I would think the high pressure side would blow up the can. If my memory serves me correctly from my schooling days the fittings are different to prevent hooking up to the wrong fitting.