Can't use my 9.0.1 iPhone with Xcode My Macbook and my iPhone are updated to the OS X 10.11 Capitan and iOS 9.0.1, but when I try to use my iPhone as a running device with Xcode, it tells me I can't use it because of the version of them.

I can't upgrade xCode (6.1). On the App Store, it tells me I'm on the latest version.
Current iOS is 9.0.2
Latest Xcode release is 7.0.1 - from the App Store
I'd try updating to those first.

If iTunes doesn't seem to think it needs updating, you could always get the .ipsw file from one of the many direct download links available [the files come directly from Apple, just the links are published separately] then hold  Alt ⌥  whilst clicking the "Check for Update" button in iTunes &amp; manually navigate to the .ipsw

One source of links is always Redmondpie - http://www.redmondpie.com/download-ios-9.0.2-links-for-iphone-ipad-ipod-touch-ipsw/