Just dont let the bag get too hot. If its hot enough that all the wax is melting off of your board and onto the bag then it is likely that you are damaging your board. If it just builds up over time then do what live4truth said and lay it in the sun and wipe it off.
Try not to leave the bag in the sun and keep it in a cool place like a basement until your about ready to put it on your car, maybe put a little water on the deck to resist the melting. Or get a bag with thicker padding is another option too.