This is how I (Kevin S) use a Black and Yellow storage box to safely store and transport 4 single modules (or 2 doubles, or 1 double and 2 singles)
First, as noted on the plastic-storage-boxes page, you have to be careful about the dimensions of the storage bin. Some have different tapper, and it is important that the taper doesn't render the bottom of the box 'too small' for your module(s). In my case, I have found that these "Project Source" Commander 27 Gal totes (sold in the USA at the blue big-box hardware store) has a bottom measurement of approximately 24.5in x 14.5in — so they will fit a standard double, with just a little bit of extra wiggle room.
The second thing I do with all of my straight modules (singles and doubles) is drill 'storage holes' on the left and right fascia. I have created a jig/template that makes sure the holes are always centered, and are 7.5in apart. This means storage can be 'mix and match' —- I can pack up the boxes with what ever modules I need for a given show. And since they are on the sides, they are never seen once the modules are setup in a layout.
For each storage box, I need two "side storage boards". These boards are made from the luna (1/4in ply) that I have left over when I build my own modules. It took me a little trial and error to find the best size, but I have found that 11in tall works best. The width can vary based on what scrap I have, but between 8.5 to 10 is what I tend to use. In the example below, it is 10.75in tall.
These storage boards also have notches cut out of opposite sites. These notches accommodate the track and uni-joiner that overhang ever module. The reason I have them on opposite sides is so that, when stacked, the tracks of one module are above (or below) the scenery side of the other module. This helps to minimize the chance that scenery elements from the different modules don't bump into each other. (In general, the area above the track is clear space, while the area above the rest of the module has all the building/trees/elevation/etc. )
If you are storing two double in a box, the process is pretty straight forward. Use two of the storage boards to connect two modules with the "tops" of the modules facing each other. In my case, I use the same wingnuts and thumb screws that I use to hold the skyboards to the modules. Place the "2-module" unit into the storage box. There is a little room at the top (as well as on the sides) to storage the skyboards. And as an added bonus, the bottom inside of the modules now also provide a little storage space where you can store additional elements (for example any removable elements or rolling stock used to complete the scene).
If you looking to store single, you just need 1 more step — connect two single together to (effectively) make a double. To do this, I use another bit of scrap. I use 2 pieces of the same luna/ 1/4 ply, doubled up to make a 1/2 'spacer'. The spacer allows room for the track & uni-joiners on the connecting side to not be damaged. Now you can screw on the side storage boards just like above.
As noted at the start, you can use this method to store/transport 2 doubles, 4 singles, or 1 double & two singles. In the example images above, I have 2 singles on top of 1 double.