You didn't say which MSD 6 box, so I've attached one of the older Install instructions for the 6400 I have saved here. Point being: take a look at the Chrysler section and while reverse-engineering the wiring match this up to the factory components.

Re: 'better or worse', I've always struggled with the following in MSD's marketing: the CD boxes provide multiple spark discharges, yey, and so apparently it makes these boxes great for racing, etc...ummm, but the docs clearly state that multiple sparks go away at about 3500 RPM...soooo benefits to racing being???

From that perspective, I would actually think that box is a better choice for a street Mopar, especially something with a healthier cam (thus a bit extra overlap and rather poor mixing), that maybe struggles a bit at a lower RPM.

No hands-on experience here, although I've got the MP branded (P4876729) MSD 6ALN box here that I'm itching to try out this coming spring!