Suggest reading the following:http://www.camaros.org/forum/index.php?topic=8140.0http://www.camaros.org/forum/index.php?topic=3143.0
As JohnZ states in one of the posts from the second link, if you install the Pertronix module in your distributor and also install a Pertronix flame thrower coil, the Pertronix flame thrower coil is designed to be supplied with a full 12 volts.
When I made the conversion on my 69RS and 66 Chevelle back in 2008, I installed the Pertronix flame thrower coil as a part of the upgrade but I did not remove the ballast wire - I went ahead and used it. Yes the voltage to the coil is reduced instead of being a full 12 volts, but for the way I drive (local cruisin', etc.) high rpm's is not an issue and the system has worked just fine using the original ballast wire supplying the coil given my driving conditions.
If you're pushing your ride to higher rpm's, etc, JohnZ's advice should be followed; i.e. feed the flame thrower coil with a switched 12v source. If you will read all the way through both of these posts, I believe you'll find the info. you are searching for.
If you upgrade the distributor but leave the stock coil in place, use the ballast wire
If your upgrade includes the flame thrower coil - recommended to supply the coil with a switched 12v source and omit the ballast wire. However, if your upgrade includes the flame thrower coil and you leave the ballast wire in place, you probably won't notice any difference under normal driving (crusing) conditions
Another way to look at it - try it with the ballast wire still in place and see what you think. You can always go to a switched 12v source later.