Bleeder valves are on the calipers. Just do the same thing you would for a normal flush after everything is back together. The purpose of flushing is to get all of the air out of the lines, so after the new pads, rotors, and lines are in place then do the flush.
For the parking brake shoes, if they are not holding the car very well, then I would go ahead and replace them.
1999 Dodge Ram 2500 Cummins Diesel
2002 Harley-Davidson Fatboy
Merlin Extralight w/ Campy Record