They do the same thing. The only difference is that the application loader forces you to check the binary in advance, whereas in Xcode 4 it is a separate button.
I recommend using the Xcode's Submit button, especially if you are using Xcode 4. The Apple method has changed Xcode 4 from Xcode 3, it looks like they want people to use it. (They made it easier in Xcode 4.) This will remove the extra tool from your workflow and may just make your life a little easier.
Just pay attention to the process when using Xcode 4. If you are doing Ad Hoc builds, you will need a second scheme for archiving with the correct code signature. If you just do local assemblies, you'll be fine with a single circuit.
Be sure to use the notes section in Xcode 4 Archives (area?) To mark which builds are Ad Hoc and which are intended for the App Store. In addition, in Xcode (not sure about the application loader) when sending you will be asked to select a code signing certificate. Make sure that this selection matches what you actually signed up with.
With these things in mind, they are essentially the same.
Moshe
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