Yup, similar boat, made even more complex by having xfire and one card not an asus so one will work with afterburner and the asus only smart doctor which is a complete pile of ****.
THe irritating thing is, if you look at I think the matrix cards, it comes with a different interface for their gpu overclocking tools, and basically is a "proper" application while the cheapo smart doctor is a truly woeful pile of crap.
I keep meaning to e-mail asus and say Smart doctor is truly terrible, the card is advertised as being over voltable simply and easy to have more performance and they have a perfectly decent application that would take probably only minutes to add support for the rest of the range too so people can use a decent application.
Infact, I think tomorrow when I'm less tired I'm going to do that.
AS yet I've found no way to get asus cu cards to work with afterburner, there probably isn't/shouldn't be a way. Reference cards were all the same so what worked with the MSI reference card worked with all the cards, the MSI lightnings are their own cards so work with the application, the Asus Cu are Asus's own design with a diff voltage regulator so doesn't work with the "standard" support Afterburner has and MSI have no incentive to make it work with someone elses card, even though I'm sure they could with next to no effort.