Hi. Yes importing from ENEX "as markdown" markdown is the generally recommended way to get your notes imported as well as possible into Joplin.
I'd say it's best to delete anything you imported, if it's not as you want it, and just try again using the markdown option. In this way you'll start from a clean slate. But yes of course first backup any notes you want to keep and you can import them later.
Let us know if this works!
Ben