If you are at the spot I think you are describing, the seams do not line up. They arms need to be sewn together with the 1/4 inch seam allowances making a little X. To get the pieces in the right spot, you insert a straight pin right at the 1/4 inch mark on one arm and keeping the pin upright, insert it into the corresponding spot on the 1/4 inch mark of the arm you are trying to sew it to. Leave the pin standing upright and put in pins on either side. You can then remove the standing pin and sew the arms together.
Make sure when sewing the arms together to stop sewing at the 1/4 inch seam allowances at the edges so you can sew in the outer surrounding pieces with the Y seams ( unless you are using the newer pattern that doesn't have Y Seams)