The resistor is eliminated from the ignition cct. When you wire up the MSD box, you power up the (i think) red wire with both the brown and blue from the ballast resistor (connect all three together). The MSD obviously needs power on 'start' and on 'run', and thats what tying the brown and the blue together do for you. After you do that, the resistor is out of the cct.
Another issue may be the tach. If you have a stock tach, you need either a tach adapter from MSD or replace the innards of your tach with a kit from RT eng.
I really liked the increased response in my car with the MSD in the bottom end. Hopefully you will like your ignition upgrade.