Do you have an antifreeze inlet? I know people do both. For me, with the antifreeze inlet that is driven by the pump, filling the lines is easy and gives me a sense of security in case there is any lingering water anywhere. If I didn't have that, I might choose to just blow them out.
Which bypass valve are you talking about? Are you talking about the hot water tank? If you are talking about the HWH bypass, I leave it in place. In the spring, I run water through all of the lines to clear out the pink stuff before putting any water back into the water heater.
As for the plug, if you are talking about the heater, I'm not sure what you are 'supposed' to do, but I leave mine out all winter.