Why not pre-wash your fabric the same way you will be washing your finished quilt?
I use my regular detergent, but a lesser amount.
Don't use any fabric softener, it can cause greasy looking spots on your fabric. Happened to me, so the fabric shop was the people who gave me this information.
I too, separate the fabrics by color, but we know we can't do that after the quilt is finished, so what is the point when we pre-wash?