|When only tailor tacks will do, it's considerably easier to tell which tail goes to which tack if you use two different colored threads. To separately mark your fabric pieces, hold the tail of the one color in one hand, and the tail of the other color in the other hand, and pull the two fabric pieces apart while holding the threads. This is even easier if you use two or three threads of each color of cotton hand embroidery floss, which is a bit softer and cushier than polyester thread, thus somewhat easier to manage.
Edited to add: Use two different colored threads in the needle. Pull the needle and threads through the mark, clip off so that there are thread tails about three inches long. When separating the fabric pieces, hold the tail of one color and the one fabric layer together, and the other colored tail and the other fabric layer together, then pull apart.