From the vise, they go onto a piece of ribbed foam at my tying desk. Then 2 or 3 of each go into my fly boxes that I carry in my Trout vest or my Bass/Salt vest. The remainder go into 6 Flambeau Zerust 3700 size boxes that correspond to the 6 boxes in my vests.
In the Trout vest I have
1) Dryfly box that holds 300 or so up to #8s. Take the center leaf out of http://fly.greysfishing.com/en-us/pr...-slot-fly-box/
2) Nymph box that holds 700 or so up to #10's. Same as above with the leaf left in.
3) Trout Streamer box that holds probably 50-75. http://fly.greysfishing.com/en-us/pr...-foam-fly-box/
4) Other box that holds Trout flies that dont go into the previous 3 boxes.
In the Bass/Salt vest I have
5) Floating flys box. See Trout Streamer Box
6) Sinking flys box. See Trout Streamer Box
Lastly, I have put a Zerust divider into each of the Bass/Salt Boxes and a 1/4 of a divider in each of the trout boxes. I don't put Saltwater used flys back in the boxes without thoroughly washing them in fresh water and drying them. The rest get dried before putting them away. I haven't had rust problems in the 2 years I've been doing this.

Tight lines,
Wade