You want to sew with the seams that face the needle on top (seams that face away from the needle are underneath). Gives you better control.
Also, the way you pin makes a difference. You really need 3 pins -- one at the seam, one in front of the seam, and one in back of the seam. The one in front of the seam is actually the most important, so there is no build-up of excess fabric by the time you get to the actual seam.
When I really need accuracy, I glue instead of pin. Use a drop of Elmer's washable glue at the intersection, push a pin through both seams 1/4" from the edge to make sure the seams nest properly, then use a hot iron on the seam. This "glues" the seam allowance in place. After sewing, it's easy to pull the fabrics apart where they were glued (if you need to).