Before spending time and money on the roof, PLEASE take the time to tape some tufts to the roof and video tape the results. If it turns out that you have poor separation, start out by getting a good baseline by doing some coast down tests as ChazInMT had suggested, that way you will know more definitively if what you have done is worth while.
My friend has a van and we tested it out (he wanted to do much the same thing) and we found that he actually had very good attachment on the roof, and extrapolating from Hucho's findings, we figured we were best off to leave well enough alone. We have tried several varients of boat tails and trailing wake tests on his van. There is much fruit to be had if you will take the time/care to test.
@FrankLee: I think I see what you are saying, the cross wind comment threw me off. And yes, frontal area is a given, but according to Hucho's findings, Cd can be measurably lowered on a sedan by raising the profile of the roof, which could mean that there is larger fruit to be had on a vehicle with a longer roof (especially if it has detached flow). Naturally, Cd and CdA are two different beasts... My friend and I found it to not be worth pursuing in his case.
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