First, you need to create your app in iTunes Connect (This is in the member center of your iOS developer account). If you've already created your profiles and certificates, then you can select the correct one in iTunes Connect. Here is where you name your app, set a price, write a description, and upload screen shots and a large icon. Make sure you fill in all information and upload all images for your app. You will know when you are done the status of your app changes to 'Waiting for Upload".
After you've created your app successfully in iTunes Connect, to generate an .IPA file for distribution (either for the AppStore or Ad-Hoc) in Xcode you need to select your Project in the file tree (at the top of the tree). Then make sure your 'Targets' is selected to the right.
Choose 'Build Settings". Then go to the section where is says Code Signing. For 'Release', make sure that the correct iPhone Distribution identity or profile is selected.
Below 'Release' it should say 'Any iOS SDK'. Make sure that it says 'IOS Distribution' next to it.
If you have the correct certificates and profiles in the keychain, you can now in the menu at the top choose Product > Archive.
If it doesn't build, then press the run button to build your project. Xcode should say that it is archiving.
After it archive's successfully, go to the Organizer. In the menu at the top choose Window > Organizer. Now click Archives.
If your project successfully archived you will see it here. First you need to Validate your project with iTunes Connect. You will need to enter your iOS Developer login info. Xcode 5 does a pretty good job of detecting the correct profiles so you should see it in there.
If your app validates then you can then distribute either to the App Store or as an Ad-Hoc distribution. Depending on which profile you have.
This is the process for distributing apps either Native or Phonegap. It doesn't matter, I've built both.
I would suggest doing it this way, in case your app doesn't validate. Xcode will then tell you what you need to do to fix. Then once you fix everything. Create a new archive and try until it validates.