I would not wash them until after the quilt is quilted and bound. If you try to wash the squares now, each one could shrink or distort in such a way as to make them very difficult to put together. Quilting will help keep the fabrics from shrinking or distorting, and will also add support for fabric that may be quite fragile.
When you do wash the quilt for the first time, I would use ***lots*** of water and Synthrapol so that any dye bleeds will be diluted and not stain other fabrics. If that doesn't take care of all of the discoloration from age and/or stains, I would wash the finished quilt with Retro Clean (
http://www.retroclean.com ).