Jeremy,
I don't know what you mean by the "bottom". The gas that is bothering you is coming from the TOP side of the charging handle. If you look at your charging handle where it interfaces with the upper receiver, you will see that the part of the charging handle that you hold onto is thick, on the top side of the charging handle where it interfaces with the upper receiver there is a half circle that is not as thick as the handle portion of the charging handle. If you look at your receiver there is a gap between the upper and the top side of the charging handle you will see where the gas slips through the upper receiver / charging handle.
It's this space on the TOP side of the charging handle that you should use the permatex. If you look at your rifle from the top you will see the half circle portion of the charging handle that you need to fill in with permaflex. It' on the top side of the charging handle.
I'm a little confused as to why you are talking about the bolt. I don't have the ability to post a pic to show you what I'm talking about. But the area of the charging handle that I'm taking about is at the rear of the charging handle (the part you grab onto) this portion is thicker than the rest, where the charging handle steps down near the upper receiver is where you put the permaflex. When you apply the permaflex your rifle should be assembled and your charging handle should be forward against the upper receiver and you will be able to see where you should add the permaflex. I hope this is clear now.