After you file

Well I've been waiting since March for my federal taxes to be accepted as well. My estimated dates keeps getting pushed out. Now it says October 21st. Problem is I owe a considerable amount and I chose to pay it electronically. Now I don't know if I'm going to get charged a penalty for late payment on owed taxes because its been delayed. I'd mail a check in but I don't want to get it withdrawn twice and wait another 4-5 months to get my over payment returned.  So how do I handle that?