Flared nut wrenches are recommended on brake fittings because the fittings are of a softer metal than a typical nut. The flared wrenches grip more area around the nut spreading the applied torque more than a standard wrench. In a pinch, standard wrenches can be used, but great care must be taken to not strip the wrenching surfaces of the fittings. The two wrenches comment is intended for non-hard mounted fittings, like a tube union, where turning a wrench on one side of the fitting can twist the tube on the other side. In these cases you should always use two wrenches, whether they are flared or not.
Jon,
In regards to your question, yes, basically. You have all your parts prepared as best you can before opening the lines. If you must leave them open, get an appropriate plug for the fittings being left open, and use a large cup or drop tray to catch the dripping brake fluid (brake fluid does nasty things to painted surfaces). And whatever you do, avoid letting the master cylinder reservoir run dry. If even a tiny bubble of air gets into the master cylinder, it will make bleeding the system significantly more difficult once you are done changing parts.