I renamed Xcode 4.6.3 to Xcode4.app then installed Xcode 5 as the default Xcode.app, Keeping both versions available. It good practice to verify which Xcode is your default using Xcode-select.
gdunham: ~$ xcode-select --print-path
/Applications/Xcode.app/Contents/Developer
example:
# switch to Xcode 4.6.3
xcode-select --switch /Applications/Xcode4.app/Contents/Developer
As the others have stated Xcode is a complete self contained package. The SDK's and new tools are contained inside the package contents. Because of this you don't need to install the command line tools just to use git, etc. You can set up aliases and use xcrun to access the command line tool inside the Xcode package
gdunham: ~$ alias git='xcrun git'
gdunham: ~$ git --version
git version 1.8.3.4 (Apple Git-47)
You personal settings are stored in your user account ~/Library/Application Support/Xcode
so they should not change.
Xcode documentations sets are stored here ~/Library/Developer/Shared/Documentation/DocSets
and shared.