If the pickups are not microphonic without the covers there is no reason to pot them. However, just putting on the cover could cause squeal by itself. You should wax the cover before putting it on the pickup. The normal procedure for that is to tape the top of the pickup cover, heat the cover and the wax (if you don't heat the cover the wax will dry immediately), pour in a little bit of wax (only very little - we only want to prevent the cover from squealing, not to pot the pickup), press in the pickup (WARNING: use gloves and safety glasses!), let it cool and solder the cover to the base plate.
Cheers Stephan