Fill the halves with stuffing or a combination of butter and syrup, then resume cooking them. When zapping the acorn squash, partially microwave the pierced, whole vegetables for five minutes, then microwave the filled halves for another two to five minutes. For baking, remove the whole squash from the oven after about 15 minutes, halve it, then return the halves to the oven for another 15 to 30 minutes.