I sort my fabric as follows:
Yardage- 1 to 3 yard cuts sorted by color
Yardage- bigger than a fat quarter but smaller than 1 yard sorted by color
Fat quarters- batiks on their own, sorted by color
Fat quarters- bundles together, the rest sorted by color
Scraps bigger than a fat quarter- stored with yardage
Scraps fat quarter size- stored with fat quarters
Scraps smaller than a fat quarter- cut into sizes I like to use and stored by size and color within the size category:
Works for me, but as others have said, everyone is different, so it may take time to discover what works best for you.
Rob