When I learned that I should put the fuller piece on the bottom, it helped with matching seams. A few times I've turned my pieces "upside down" to get the best fit. Also, it is sometimes easier to "correct" the intersections after the fact. I go back and rip out a few stitches on either side of the intersection and am able to get things to match up. Another quilter taught me that trick.
As I have gotten more experience and can make my seams equal in width (I aim at the quater inch), that has helped too. One other "tip" is to be sure you are squaring up your blocks --it is tedious sometimes, but well worth the time it takes and pure joy to watch the seams match so easily.