With the update to the 1.3 version of GameMaker: Studio, certain changes have been made to the way that apps are built for iOS. Previously you were required to use the Application Oven to build the YoYo Runner for testing and for building a final IPA for submission to the store. This is now no longer necessary, and the toolchain has been simplified.
Note that if you are new to iOS, you can find further information about the themes covered in this article from the YoYo Games Knowledge base article "Develop And Distribute To iOS".
When testing your game from GameMaker: Studio, you no longer have a single YoYo Runner for all games. Instead a new runner is created for each game being tested, which means that things like in app purchases and extensions can be tested correctly. However it also means that the first time you test your game, you must have it connected via USB to your Mac, and it must also be visible over Wifi.
Once you have GameMaker: Studio communicating with your Mac and your test device is connected via USB, you can go ahead and test your game for the first time - this will create the game runner and push it to the device.
Once you have successfully tested the game for the first time, you can then unplug the USB cable if you wish, and simply use the YoYo Runner to download the game files over Wifi. Note that if you want it to test a final executable on your device you must have the device connected via USB as Wifi will not work.
Before you can upload the game to the App Store, you will need to have made an App Store listing for it, and the listing should say that it's "Ready to Upload binary". You can find full details on how to do this from the helpdesk article "Getting Your iOS Game On The App Store". With that done we can now go ahead and use GameMaker: Studio to create an Xcode project file, and it's this project file that Xcode will then use to create an IPA for testing or to submit to the App Store.
When you are ready, make sure to revise the Global Game Settings and be sure that the Bundle ID matches that which you created for the game on the store, and check that the game options for orientation, etc... are correct and that all the icons and splash screens required have been added
You do not need to change the provisioning profile used here for the Distribution profile, as that will be added later in Xcode, so make sure that it is still set to the Development Profile and Developement Certificate. When you are happy that it is all correct, make sure that your PC is connected to your Mac and test play your game to make sure that it works on the iDevice correctly.
When you are ready, click on the "Create Executable" icon at the top of the GameMaker: Studio IDE and select a location to save the project to. This is a security measure and the files saved to your PC are simply a copy of those that will be used by Xcode to build your final game. GameMaker: Studio will now build your game in Xcode.
In Xcode you will see that your project is now listed:
There may be a warning shown in Xcode (a yellow (!) will be shown), but these can be ignored, and from here you should now go to the Xcode Organiser, which you can find under the "Window" drop down menu. You need to select the Archives tab.
This will show all the apps that have been built on the left, then when you select one you'll get the details for the app as well as a list of all build that have been made. Now you should select the game build that you wish to upload to the App Store and click the button marked "Distribute". This will open the distribution wizard and you will be asked by Xcode how you wish to distribute. If you only want an .ipa for testing then choose Enterprise, otherwise set it to Store.
Next you will be prompted for your Apple ID and Password, after which you will need to select the Distribution Profile for the game that you are submitting. With that done, you can complete the wizard to upload the final binary.
If you chose a Store publish, Xcode will launch the Application Loader in the background and test then send your game to the store (if you chose Enterprise to publish, Xcode will show you where your .ipa has been saved).
If all has gone according to plan, and after a few hours have passed, the status for your game on iTunes Connect should change to "Waiting For Review". this means that the upload has been a success and your game will be reviewed and published when ready.