Either method, if done properly, is effective and viable; like a lot of things, it comes down to personal preference as much as anything. I use the blow out method, since it's less expensive (as I already had a suitable compressor) and doesn't leave lingering antifreeze to make fresh water taste bad.
If you're talking about the water heater bypass valves, leave them bypassed until you put the RV back in use. You want to avoid getting antifreeze into the water heater if possible because it takes a lot of water and time to rinse it out on the other end when you dewinterize. It doesn't make any difference in terms of preventing freeze damage one way or the other, though.