Bubble’s instructions are fairly simple & straightforward. The major hurdles are registering as a developer with apple. If registering as a company this requires you to get a DUNS number from Dun & Bradstreet, which is a 2-4 week nightmare. I’ve read that its more efficient to apply via Apple’s site for a DUNS number, instead of DNB’s website directly. If you’re submitting as an individual, then there is no need for a DUNS.
When you request the zip file from bubble, they usually reply within a few hours or less. Their reply contains all the instructions you’ll need to get going. You have to replace various PNGs with your own app icon/ logo. You then rezip that file and upload it to phonegap’s console. Phonegap also requires a few Apple keys/certificates (I can’t remember all the details exactly.) Phonegap gives you an ipa file, which can be opened on your iPhone via iTunes.
If I’m not mistaken, your bubble app is essentially a webpage bundled into a native app. So any changes you make are immediately updated in your app, with a few exceptions of app icons, loading screen, and probably a few others.
You should only need to request the zip file from Bubble once.