One question we often get is "Why do you attach eyes, nose, mouth etc after stuffing, and how do you do this so that knots aren't showing?" So here is a tutorial that is perhaps not easy to convey with pictures only or words only, but hopefully with the two combined it will make a lot of sense!
To answer the first part of this question, attaching applique pieces after stuffing a softie has two big benefits. The first is that a softie can be quite unpredictable and depending on fabric used, width/size of fabric pieces, firmness of stuffing etc, the end stuffie can be quite different in proportion than you initially thought. With adding details after the toy is stuffed you have great control over getting the perfect placement and having a balanced toy. The second reason is to avoid distortion or damage to your applique pieces. One concern when doing your applique first is that the stitches could become damaged or pulled by your stuffing tool during the stuffing process. Another concern is that the fabric stretches (as it will do if you stuff firmly) and this may pull your stitches or even make holes in your backing fabric. Of course this is not a hard and fast rule but it is the way we usually like to work.
For the second part of the question I will need to employ the help of some photos. For this tutorial I am going to attach a nostril to this unfinished "Drake the dragon" by "sinking" the knots....
Now thread your needle with the specified stands of embroidery floss (In this case I am use 2 stands of black floss), and tie a knot in the end as per usual. I recommend that you tie a double knot in the case of 2 strands or as a rule, ensure that the knot is roughly the same width as your needle.
...this will cause the knot to pop through the weave of your fabric and "sink" inside the softie. You need to ensure that you do not tug too hard or violently or your thread will also come through the top side and you will need to start again.
....Now you can complete the sewing required on your softie. Of course this is not limited to just applique but is also the method to use for any stitching or attaching of limbs/ears etc etc....
Once you have completed your stitching (in this case, I have button-hole appliqued the nostril in place) and are ready to take your last stitch, tie a knot close to the base of your thread. Again ensure that the knot is roughly the same width as your needle as shown.
Again your thread will snag when the knot reaches the fabric. Tug the thread again to sink this finishing knot into the softie...Cut the thread right at the fabric and this cut end will also sink into the toy..