Will the MAS prompt me to keep my Xcode 5? I have Xcode 5.11. If I try to install the newest (6.0) Xcode from the Mac App Store, will I be prompted to keep my current Xcode?
No, Xcode 6 on the Mac App Store will replace the existing Xcode installation. Only the Xcode betas install separately (by default) and only downloading Xcode from developer.apple.com and doing the install manually (by copying Xcode from the DMG to /Applications) will prompt you to replace or keep both.