The key here is just be consistent! If you cut using the lines on you mat then continue the whole project using the mats lines. If you use the ruler, use the same ruler throughout the whole project to insure better accuracy.
All rulers do not match. And usually they do not match the lines on your mat. My Fiskars ruler lines do not match exactly to the lines on my Omnigrid rulers. Albeit the difference is minute, when working on a project that bit of minute will rear it's ugly head.