Overlap your two pieces about 3 inches.
Make a serpentine cut all along the overlapped portion.
Before you cut, make sure you have both the right sides up before you cut. How to tell? Most needle punched cotton bats have a right and a wrong side. Take a pin and poke it in the batting 5-6 times. Notice the resistance or lack thereof. Turn the batting over and repeat. The side with the least resistance is the top. You don't want your sewing needle to stitch into the resistant side when you are quilting.
Remove the little strips and you have a perfectly matched joint.
Butt up the 2 edges on the ironing board.
Iron on a 3 inch strip of lightweight interfacing. Someone actually makes a product on a roll for piecing batting, I have only heard about it though.
You can do the same with a polyester bat, except you have to zigzag or whip stitch the joint together. Polyester does funny melt-y things under the iron.