There are multiple ways to do this. You could either create a custom taxonomy called something like “show_on_home” and then, just like a category, you would choose an option when publishing the post and the just add ‘show_on_home’ => ‘true’ to your query.
Or, if you really want to use ACF to do this, you could just use a conditional statement to hide some of them. Something like this:
if (get_field('show_on_home')) {
Put your loop here...
}
That is sort of inefficient though because your still loading the posts with the loop, and then just hiding them.
The better way to do it, although a bit more complex, is using meta_queries in your main query. I would start here to learn about those: http://codex.wordpress.org/Class_Reference/WP_Meta_Query
