This is how I do it.
Cut your pieces to size, the lighter color is always cut 1/4" larger.
Remove the backing from the darker color covering, leave the backing on the lighter color.
Tape the two pieces together, darker color on top, with small pieces of masking tape to maintain alignment. Tape every 6" or so.
Place a piece of 1/2" square balsa on your work surface and place the joint on top of the balsa. The goal here is to keep the heat away from the covering except where joining.
Starting with low heat, tack the top piece to the bottom. Skip back and forth, eventually removing the masking tape.
After the complete joint is tacked together, increase heat and firmly iron the two pices together while still on top of the balsa stick.
Clean the back of cover with a tack cloth before removing the backing from the lighter colored sheet.
I usually layout the pattern of the airframe with a fine point Sharpie pen, you can normally see through the ligher colored Monokote to locate the covering on the airframe.
Be careful with the heat gun when shrinking over open bays, I find that the iron is easier to control the heat.