extra thermostat, electric dampers and 1 furnace
If the main thermostat doesn't live in one of the bedrooms (probably doesn't), you'll lose the feedback loop that makes the thermostat work.  In other words, the thermostat will stay cold, and keep calling for heat, while the bedrooms are broiling.

If the problem is that the bedrooms are always cold (assuming winter), and you want them warmer, another shot at balancing the system is probably in order.  Get aggressive (I have one vent in my family room where I blocked the entire thing with a sheet of cardboard with one 2" hole).  Try blocking 50% of the area of the register with cardboard behind the grate.  Do this on the vents in the warm part of the house, and make sure the bedroom vents are open all the way.  This is a weekend project.  You'll put some baffles in, wait an hour or so, make some adjustments, wait, rinse, repeat.  Buy a couple cheap thermometers and leave them in different parts of the house so you can check on them.

Just be careful not to block too much airflow.  You should take the temperature of the air coming out of the vent closest to the furnace before you start.  If it rises notably after you're done, you might want to undo some.

Also, if there's not a decent gap under the bedroom doors for airflow, leave the doors open, trim them, or install a through-door vent.  If you sleep with the door closed and there's no way for the air to circulate out of the room, it won't get enough airflow, and the room will get cold.