I tend to group first by type of fabric - batik, flannel, home decor, regular cotton (Christmas, Asian, kids, and extra brights get their own stacks)
Then within each grouping I sort by color. Within the various color stacks I at least start out with them going from light to dark within the stack. 😉 Or I may have a dark stack and a light stack for that particular color.
My folding method is selvedge to selvedge then fold again the same way. Then fold that crossways however many times to fit shelf. By looking at how fat the folded piece is I have a general idea how much of each is there. If I have two identical FQ for instance, I will fold one inside the other. Also any sizable scraps are folded in with the main fabric.
Works in progress are put in small basket/crates with all the relevant folded fabrics plus a zip bag with any pieces that have been precut but not yet stitched.
I also have a couple groupings of fabrics set aside but not yet cut that are destined for specific future projects in baskets like the WIPs.