If you're talking about a late-model computer controlled small cap HEI system the 5462 will patch into the factory system. See figure 7 of the instruction:
http://www.msdignition.com/pdf/frm23950.pdf
Note that the 5462 is NOT a CD (capacitive discharge) ignition system- it's still inductive, although it is all in one box.
If you're using an earlier large cap non-computer controlled HEI then you are probably better off getting a complete ignition with the boost retard function already built in like the 6462. This system will also work with the computer controlled small cap HEI system. And this one IS a CD system, it's jsut got the boost-retard function built in:
http://www.msdignition.com/ignition_7_6462.htm