I can't guarantee that this is the "right" way but it's how my mother taught me -
Take a long double length of thread and put it through the needle doubled again (you will be sewing with four strands, the thickness holds in heavier fabric more firmly, if you are sewing finer fabrics do this with two strands)
take a small stitch through all layers where you want your mark and leave a good 1.5" tail sticking up from the surface of the fabric
take a second small stitch (I usually form a cross stitch on the back)and this time leave a loop 1.5" long
snip of the thread with a 1.5" tail
now you can "pop" the pattern off the fabric carefully to leave just a small hole
ease the layers of fabric apart and cut the stitches so that there is a "tuft" of thread at your mark on each fabric piece
You will find it best to do all your tacks on each piece before cutting any. You can use different coloured threads for matching tacks if you think that will help. The tacks are a good way to use up cheap cotton threads but be careful about using strong colours as you don't want to have any colour transfer, and I do not recommend poor quality poly thread. If you need to mark four pieces you can make the loops/tails longer but I would then take three stitches for added security. And remember to match your fabric weight to the number of threads and needle size - four strands of cheap thread sewn with a "crowbar" will leave holes in silk!
The cut tacks will easily pull out when you are finished with them, but try to avoid too many machine sewn tiny stitches through them as this can make removal difficult.
There are many experts here who can probably describe this better but this might help get you started until you hear from them.