I agree with those who recommend not prewashing. In terms of shrinkage, fabric (including flannel) shrinks very differently after being quilted than before. What I would recommend is quilting a large X in each block. This will stabilize the layers so they shrink together.
As for colors bleeding, I like to do the first wash with Synthrapol in a machine that uses a lot of water. Most domestic front-loaders do not use enough water to dilute dye bleeds. Domestic top-loaders and large front loaders at laundromats use sufficient water. Very few fabrics bleed these days, but it's always good to have insurance. Synthrapol helps keep loose dye particles suspended in water so they get rinsed away instead of settling into fabric. Although it's most effective with hot water, for this kind of flannel quilt I would use cold water and add a few color catchers along with the Synthrapol. That should be more than adequate, especially if you use lots of water for that first wash.
One thing to watch out for with flannel is pilling. To minimize pilling, always wash the quilt by itself and preferably in a front-loader. Top loaders that have a central agitator posts are hard on fabric because of the rubbing of the quilt against itself. Avoiding that kind of friction will help minimize pilling.