the easiest way is to make one row of pattern all the way across the width of the freezer paper, then, put a size 16 needle in your sewing machine and use a long stitch with NO THREAD to sew along every line of the entire pattern to perforate ... buy or make chalk dust.... (quilt shops usually have the dust, I usually just put chalk into a clean and empty pencil sharpener and just sharpen into dust... buy the big packs in teacher or school supply shops...
pin freezer paper into place (weight down in between pins but AWAY from lines), sprinkle dust down the length of the pattern, use makeup brush to brush into holes and remove paper carefully, folding and pouring chalk residue back into your bowl or shaker (i use a large flour shaker because I can control where it goes better)
lay paper flat to await the next time you roll the quilt
one paper pattern saves time making them, is not destroyed during the chalking process, can be rolled up for another use AND leaves you with a chalk pattern to follow that will brush away with a damp washcloth in seconds when finished.
I have had a flynn frame for 20 years now and it is one of my favorite tools... i have a longarm but i don't do all my projects the same way and this is one of the best... i love the fact that i can do some on the machine, but I can also finish fine, noticeable areas by hand while leaving it on the same frame, even moving it back and forth as i pass the point for the hand work (the frame fits my rocking chair arms perfectly.... and when you finish for the day? stand the entire, loaded frame behind the door...no storage problem...I even took 3 heavy duty trash bags, cut off the ends of 2 of them, then sewed one cylinder to the next, and then both cylinders to the last, WHOLE bag.... this gives you a lightproof and dustproof 9 ft long bag to slip down over the frame, quilt and all... it's open on the bottom, no condensation problems, just protection for the project you don't get back to this week...you can trim the extra length off if you like..