The exported .html file can be renamed to whatever you want (or simply exported with the index.html name). It is only the name and contents of the .hyperesources folder that must remain the same.
There are some specific tips on this post by @daniel. Searching the forums will reveal other tips.
Beyond this, there’s nothing too special about Hype’s output that causes issues with PhoneGap, so their documentation should directly apply! Of course you’re welcome to ask any specific questions as well.