I'd suggest Durham if your partner is going to Duke. Chapel Hill/Carrboro is a very nice place to live, but you'll eventually feel the smallness of those two towns. I'm still at UNC, and I live in Durham. I don't commute to campus very often, since I'm barely on campus. But the commute isn't bad. There are bus options between Durham and Chapel Hill, either Triangle Transit or Robertson Scholars. The latter is a bus line that runs exclusively between UNC and Duke, and is free for Duke and UNC students. You can also drive part of the way to a park-and-ride lot, and then take Chapel Hill Transit, a free line that runs throughout Chapel Hill and Carrboro. Duke has their own bus line that will take around campus, but not much beyond. There's also the free Bull City Connector, which runs between Duke's campus, through downtown, to East Durham.
As for where to live in Durham, there are plenty of apartment complexes near Duke's campus, if that's what you want, generally around Erwin road. But if you want a house, I'd check out the following neighborhoods: Lakewood (parts of this neighborhood, at least), Old West, Watts-Hillendale, or Trinity Park. These are all relatively close to Duke's campus, though the rental market is very competitive. If you're willing to be a little further from Duke's campus, I'd recommend Northgate Park, Duke Park, Old East, or Cleveland-Holloway. The last two are probably the least gentrified of what I have mentioned, and are generally going to be cheaper.
If you do decide on Chapel Hill/Carrboro, I'd suggest going with Carrboro. You can find a great place to live in Chapel Hill, but you're probably going to be living near a lot of undergrads. Carrboro's vibe isn't for everyone, but you're generally going to be living around a more age appropriate crowd.
As long as you avoid apartment complexes, you will generally be within walking/biking distance of things to do, either in Durham or Chapel Hill/Carrboro. Durham is more spread out, but that's because it is also bigger. So if you live in Durham, you will drive more often within Durham. But if you live in Chapel Hill/Carrboro, you will find yourself driving to Durham, Raleigh, etc. more often.