I'm a believer of prewashing yet I hate to iron! The big pieces are the worst. Try to get it out of the dryer as soon as it is almost dry, do not dry all the way -- that's hard enough with regular fabric and would be a bear with flannel. And while others may not recommend it, with flannel especially I'd have steam in my iron or at least my spritzing bottle handy.
When I have yardage like this I put my ironing board the long way along my couch, using the couch to hold the draped fabric. I first iron along each selvedge edge the width of the ironing board and then go through the middle.