I'll try to explain. Let us assume the pattern is a flower, stem and leaves. The whole pattern must be marked on the reverse side of your background fabric. Using a light box or window, tape the pattern down first and then center the background over the pattern. Use a marker with a somewhat fine point or light pencil marks. I prefer to use the Fixion pen. I also use the Clover pen if marking on lighter fabrics. Both of these disappear when touched by an iron.
Since the stem is to be stitched on first, cut the stem fabric large enough to cover the entire stem. Stick pins thru from the back to give an idea of where the stem starts and finishes. Pin in place from the top side. Hold up to the light and make sure all of the stem is covered. Now, from the back side baste along both sides of the stem using -1/4" long stitches. Turn over and see the basting stitches. Using your Fixion pen, draw a dotted line between the basting stitches. This dotted/basted line will be your turn-under line. Trim excess to 1/4" from the dotted/basted line. Clip inward curves as you come to them. Using needleturn method of applique, stitch the stem into place, clipping the basting thread out of the way as you stitch.
Leaf, assuming it is under the flower petals, therefore to be stitched first. Any area of the leaf that is overlapped by a petal does not need to be needleturned. Using big stitches secure this part. Otherwise, cut a large piece of green, stick pins from the tip and base of the leaf (and width if necessary) for placement, baste as before, make dotted line, trim, needleturn. -- Leaves along the side of the stem are usually free standing (for lack of a better word) and can be done whenever.
Petal, chose one that has overlaps, working each petal from background to the forward as you progress to complete the flower. The center of the flower will be last and should cover all of the petal ends.
Note: the design will be the reverse of the pattern; think negative/positive and make changes as necessary.
When the entire design is appliqued, press (no scrubbing) the design into a towel so you don't crush the applique. Spritz lightly with starch, if you want. Touch up any Fixion pen marks that remain on the right side with the tip of your iron.
Stand back and admire.
PS: Fixion pens are available at LQSs and come in many colors. I have black or navy and the Clover white.
I hope this is clear. If not, please ask and I'll be more prompt in responding.