Today in the spirit of protecting my projects from her and vice-versa, I have my stitching categorized in Ziploc bags for every project that I have unfinished. In each bag I have the 1) fabric project 2) the pattern 3) sometimes the hoop and 4) the thread.
I always leave my magnet with my needles and scissors separate.
Mostly the projects storage can be standardized, but the threads are always the tricky bit.Sometimes on the projects, the thread can't be easily managed on a thread sorter. On the larger more complicated projects, I use Floss-Away rings with the baggies. If it is more convenient, sometimes DMC threads compactly intact in their original skeins, sometimes I have them on a DMC Floss Bobbins.
This is how I do it: