I think it largely depends on the type of plant you have, and your personal preference XD
But my experience with plants like this is anubias, and I just attached the plant to a lava rock. I used flavor free dental floss to initially adhere the plant to the rock. The roots will eventually attach themselves to the porous rock.
I did the the first idea that you have, once the roots were attached enough to remove the dental floss. Most of the rock was buried in the substrate with just a little bit of it above it.
But like I said it depends on the plant. My experience is just with anubias which generally prefers to adhere itself to some sort of anchor, like lava rock or drift wood.
Simply a newbie to the fish world, looking to get her feet wet...