It depends. My cleats are plastic on the outside (or something like plastic) so I just took a wet paper towel and some lysol or something to them. If they smell really bad then just spray them with fabreeze or some Dr. Scholls spray. If they are cloth on the outside you can still use a wet paper towel but it can be a real pain. It should only take about 15 minutes though. Keep them out of the washing machine.

I would just take out the insole and wash them. You'll have to wash the shoes themselves by hand.