Well, I could tell you how I organize that little stuff, or I could say how I wish I could keep it so those things never go AWOL !
I try (key word, try) to keep multiples of those things in various places where I know I use them. At my sewing desk, I have a drawer. I also have a pegboard above it. I also have a couple of eyeglass cases that I like to fill with a small bobbin of thread, hand needle, some clips, little scissors, a thimble, a piece of batt to hold my needle. Those cases should (ahem) stay in the drawer of the end table where I am most likely to sit and hand sew while watching TV.
But I have spent probably 2 years of my life searching for little stuff that has a home but often decides to travel without a stamped passport, so to speak.