Most times you can plan your seams by pressing one to one side the other to the other.
However, there are time when you sew a row and seams will be going in the same direction. In this case, I simply fold one seam over the other direction as I am sewing in order to make them nest. Remember that no one is going to rip your quilt apart in order to see which direction you've sewn your seams, so sew them and press them in whatever direction you want in order to get it as flat as possible.
Some seams may even go in both directions!
And if the intersection is really bulky, just open up those seams and sew it that way.
Another trick I use for bulky seams is to grab a little paint brush and paint on some spray starch just on the bulk and press it with a hot iron. That makes the bulk lay very flat.
:-)