Xcode fully supports git in a very nice way.
As for building the bitcoin App:
I broke the project into two repositories:
1) git@github.com:udibr/bitcoin.git
 is a fork out of the original bitcoin repository and in it I used #if TARGET_OS_IPHONE || TARGET_IPHONE_SIMULATOR to mark my small changes.
2) git@github.com:udibr/bitcoinApp.git
is the App itself and this is where the Xcode project file for both repositories is held: BitCoin.xcodeproj

In addition you need to build several other packages for iPhone. The above is just an overview, the exact steps are described at
https://github.com/udibr/bitcoin/blob/master/build-iOS.txt

Good luck, Udi