Where you place the ruler (right/left/center) of the printed line depends on the brand of ruler. The olfa rulers with the wider yellow lines may be more difficult. Creative grids has a thinner line, but some find the markings confusing. Olfa has a newer line of rulers, Olfa Frosted. Very simple, thin lines.
also, if possible, you need to use the same ruler, or at least the same brand of ruler for your entire project.
Finally, don't know how you were determining your quarter inch seam. here's a link to a common method:
http://www.quiltingboard.com/tutoria...ce-t89997.html