How do I build an xcode project for the itunes store?

Try this:

Prepare a new provisioning profile for App Store

1. Make sure you have Ad Hoc distribution working OK.
2. Go onto the Program Portal > Provisioning > Distribution
3. New Profile button
4. Distribution Method: App Store
5. Profile Name: MyApp App Store (or whatever)
6. App ID: MyApp (you have already created one right?)
7. Submit button

Set up the new profile/configuration in XCode

8. Download the certificate (you can click on the Distribution tab to reload that tab while it's being generated) and load it into XCode
9. In XCode, open your project and go to Project > Edit Project Settings (or double-click on the first item under Groups & Files panel)
10. Configurations tab, click on your existing Ad Hoc distribution configuration, that already works, and click Duplicate button. Call the new one "App Store"
11. Click on Build tab, then under Code Signing > Code Signing Entity in the popup choose "iPhone Distribution - MyCompanyName" under "MyApp App Store"

Build & Upload to iTunes Connect

12. Clean all for good luck, then set Active Configuration to "App Store", build & go. Test it on your iPhone.
13. Find your built app in the Finder, in your project directory > build > App Store-iphoneos > MyApp.app ... right click and "Compress MyApp.app"
14. Upload resulting MyApp.zip to iTunes Connect.

A Universal Binary has nothing to do with it. To distribute through the App Store, you need to create a Distribution provisioning profile. The iPhone developer portal has step-by-step directions for this. look under the "Distribution" tab.

I followed the instructions listed by sbwoodside but had problems with the last part (Build & Upload to iTunes Connect). I realized that the built version didn't run on the device. This is what worked for me:

Build & Upload to iTunes Connect

• Clean all for good luck.
• Go to "Edit Scheme" and in the Archive menu, select the App Storebuild configuration.
• Select iOS Device or a specific device in the drop down menu and goto Product->Archive.
• Once Xcode is done archiving, it will open the organizer window andshow the archives section. Select the last archive and click"Submit".
• You will be asked to enter your distribution certificate. Selectthe one created for the App Store.
• XCode will upload the app to iTunes Connect without the need ofusing Application Loader. For this to work, the app has to be in"Ready to Upload" status in iTunes Connect.

You won't get to test the last version with the device. Therefore it's best to make an ad hoc version before to be able to test all features and once everything is working, duplicate the ad hoc configuration for the app store.