That depends on what you mean by not being in the proper place. Do you mean you dont have enough stand off's for each hole in the motherboard? Then yeah, you can run it, just make sure its supported in important places (places of stress of plugging in cards, power, etc). However if you mean you have stand offs under the motherboard that don't line up with any holes, that can be very bad. You don't want metal to contact with parts of the motherboard, thats the whole reason the stand offs exist.