I usually cut cut up a 1/4 yard of inexpensive muslin into 2" squares using my rotary pinking blade. That way when I get new fabric I can mark the yardage on the square and pin it to the fabric. I usually also mark whether it has been washed or not.
When I have used a fabric for a project I alway put the loose left over pieces in a plastic bag. If there is still a fair amount of yardage left I pin the bag to the inside of the folded fabric. That way it all stays togther.