Can fondant be frozen before covering the cake?
There's really no point to freezing them, because once you take them out of the freezer, they start to accumulate moisture, which will cause the fondant to melt, or at least get all goopy, as you said. The only way to avoid this when you freeze them is to wrap them airtight, but you have to leave them totally wrapped until they thaw, so why bother? I would just air dry them for a few days and apply them to the sides of the cake. Better yet, why don't you do this with gumpaste instead of fondant? That will dry a lot faster and better and won't lose its stiffness when you apply it to the cake, so you'll get a more box-like effect.

I just used this method for a wood crate and found this tutorial : http://sugarsweetcakesandtreats.blogspot.com/2010/04/wine-bottle-in-crate-cake.html

I would to ensure it dries firm and is strong enough to stand on end. I can't remember the exact amount - I just added a little bit at a time until I noticed the color start to lighten, slightly. Once dry, I attached the panels to a fondant covered cake with a little buttercream. The panels stayed in place and remained firm. When it was time to serve, we just removed the panels and then began cutting.

the precolored fondants are so saturated with color, you can also add a little gumpaste to your black fondant without it affecting the color. Not sure what brand you're using, I'd used Satin Ice for this purpose as it will dry firm. I did for the panals on my shoebox cake and my Alamo cake - both times they were ready to use within 24 hours (flipping a few times during drying time).then measured the crumb coated cake and cut out the fondant panels with those measurements adding about 1/3" on both the front and back panels (cut the two sides exactly as measured).The panels dried for 48 hours (they were still a little flexible, but stiff enough to work with). then cut out four strips of black fondant and put them on the four corners of the cake (wrapped around the edge). it helped because any small gaps between the sides of the panels were largely disguised by the black underneath instead of white BC showing through.

I didnt have to re-cut/re-size the panels once appllied to the cake. I found that with the black fondant underneath and by simply applying or scraping off BC where needed to make it fit, it all worked out. Oh ya, I applied gumpaste/tylose glue to the fondant corners so that the panels fit nice and tighltly.