You can read about adding custom JavaScript for ACF here http://www.advancedcustomfields.com/resources/adding-custom-javascript-fields/
beyond that I’d be of little help. I have avoided using custom JS. Basically you’d need to detect the change of the end date field then get the value for the start date field and then alert an error if it’s not later.
Like I said, I don’t know exactly how to do it. I could figure it out if it was necessary. while doing this would be a nice addition, it it wasn’t included in the requirements, I would not go out of my way.
You might suggest it, but knowing what is in the conditional logic and what it can do making this part of ACF isn’t all that likely.
