First off, let me say you have done a great job with the hearts and it's such a pretty little quilt. There is one lucky little girl that is getting it!
Now, as to the middle squares....I would just stich/ditch around them as to not take away from the square.
I hand sew my labels on when I'm done. I use a little Lite Heat N Bond to hold it steady, then whip stitch it in place.