Here's what I would do:
After washing to preshrink the fabric, dry in dryer, iron, then fold selvedge to selvedge. Here's where most folks rush through - match up the selvedges all teh way across so that bottom is straight and if you end up short on either end. make your straight cut. Then fold fobric over itself until you have about 24' showing then cut into 6" strips with your roatary cutter and 6x24' ruler.
Continue unfolding fabric and cutting until whole piece is cut into strips.
Then, place two strips ,one on top of the other lengthwise on mat, measure into 6" and cut through all layers. Do this until all pieces are cut.
You should prabably put a new blade in before cutting and another when all done. I have found cutting flannel is hard on blades even more so than fleece, I think.
Hope that all made sense.