Rhe, does your intersection tend to overlap, or is there a little gap where they should meet?
If they overlap, do like Ritzy said, and put the seam that is pressed towards you on the top. The presser foot will cause the top fabric to be pushed forward a little.
If there is a little gap, put the seam pressed towards you on the bottom. The presser foot will cause the top fabric to be pushed forward and close the gap.
In fact, if you can adjust the amount of pressure that your presser foot puts on the fabric, that may be what's causing your problems.