This may not be for everyone, but I'm a cheapskate and do the following.
I make shelves out of cardboard & 1" foam sheets and place 5 or 6 layers of them in Sterlite 14"x 11" x 6 1/4" plastic boxes.
To make the shelves, I start with two layers of cardboard (corrigations at right angle) cut to fit the bottom of the box (the box gets bigger towards the top). This will be the base. Glue these together with white glue and put a heavy book on the cardboard until it cures A serrated knife and the edge of a table works for cutting the cardboard.
Take a sheet of 3/4" thick styrofoam (Home Depot store- used for insulation) and paint it both sides with spare latex paint. After it dries, mark 1" wide stripes on it (Sharpie pen) and cut it into strips with the serrated knife. Do it outdoors or in the garage as it will generate beads of static-charged foam. Then paint the white sides with the latex and stack them up to dry.
Now white glue the foam fingers onto the cardboard. Glue all the edges first and then the fingers with spaces wide enough to hold your ships. You can use little chunks to make individual compartments.
What you have are very light trays that keep the ships from rattling around and are stacked inside of the box. You can lift them out, you can write on the foam as to what ship is in what spot.
I also mount the ships on blue painted "popcycle sticks" from a craft store. You find these in the section where they have wooden stuff for assembling and painting. There are several sizes- I just use a DD DE size and a all other ships size. Paint one side to match your ocean matt and write the ship ID on the reverse side. White glue the ship on one end of the stick and then paint a white ship wake from the bow and stern.