I'm using "Custom Smilies" plugin and would like to add the smilies to the Comments reply/post area.

How would I add the Custom Smilies to Atahualpa 3.4.6 Comment section?

Thanks in advance.

have you tried following the install instructions and using it?
note that the pluggin is compatiable to wordpress 2.3.3 and hasn't been updates since January of 2008