In Rhino 5 you will need to explode the polysrf to assign separate materials. We have been working to make this easier and in Rhino 6 you’ll have the option of sub-object material assignment so exploding won’t be necessary. With that said, I’m not sure if this sub-object material assignment info will export in the file format you’re using. If you have a v5 license and registerd on the forum with the same email associated with that license, you should be able to access the Rhino 6 WIP to test it out. Ctrl + Shift when dragging a material to a plane on a box would assign that material to just that side.
Here’s a link to the v6 WIP page…
http://discourse.mcneel.com/t/welcome-to-serengeti/9612