I'm assuming you are talking about "safety pin spinners" the type of lure common for large mouth bass fishing. I've found a great solution for storing these on a canoe trip.  I use Lure Keepers.   (You need to Login or Register These are designed to cover the lure when it's on your rod so they don't tangle or accidentally hook someone. They are great at that but also will hold 2 jig spinners each when stored in your "box". 

Personally I use a small compartment plano box for lures and then use a foot long cordura soft duffle for misc. items and put the lure keepers in there.

I also use an electrician tape plastic circle box to store my pike leaders in.  Works great.