For KLX style plastics you can run it exactly like a bike bike and suck the air inthrough the handles in the side plastics.
As mattbomers said, a bit of radiator hose to up under the seat with a filter on it and then shroud it with an old water bottle with a few holes in it and the bottom cut out.
We did this for the motard Nationals recently when it peaced down raining and we were having no end of troubles with water being sucked in.
If you don't have KLX plastics, still do the water bottle shroud with the bottom cut out, doesn't work as good but will keep the engine free from extra dust and crap for about 3 times longer than a regualr filer.
You may find that you will need to re-jet slightly as all these cover-ups do restric a bit of airflow.