Melissa,
I fold my yardage selvedge to selvedge and then roll it around my big ruler and fold it in half, this way all the yardage is folded the same and I can tell approximately how much of it I have by the thickness of the fold. I too sort by color and that is how I normally look for fabric, if you get one of the plastic tubs or those clear plastic drawers, you can just stack your yardage in them and store in the closet...this is what I do.I also leave the fold showing towards the front so I can actually tell what fabric it is without opening the drawers.
Hope you are doing well.