I didn't find the answer on Apple's site, but I did finally find it elsewhere. Hard to justify how awkward this entire process is to upload to the store, but below are the key steps (copied from a post elsewhere) related to this specific question. Hope it helps future frustrated developers!
P.S. I used my "release" setting to duplicate rather than ad-hoc which I had not created (this relates to step 3 below)
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Set up the new profile/configuration in XCode
1. Download the certificate (you can click on the Distribution tab to reload that tab while it's being generated) and load it into XCode
2. In XCode, open your project and go to Project > Edit Project Settings (or double-click on the first item under Groups & Files panel)
3. Configurations tab, click on your existing Ad Hoc distribution configuration, that already works, and click Duplicate button. Call the new one "App Store"
4. 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
1. Clean all for good luck, then set Active Configuration to "App Store", build & go. Test it on your iPhone.
2. Find your built app in the Finder, in your project directory > build > App Store-iphoneos > MyApp.app ... right click and "Compress MyApp.app"
3. Upload resulting MyApp.zip to iTunes Connect.
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