Jungle
Well, you can make the eyes transparent, Feareh's Tutorial might help you with that.About the hole in the head, is that something that has happened while you tried to remove the eyes?
A screenshot of this situation would defiantly help. If you could show us a picture it would be easier to help you ^^
Firstly there is a hole in the top of the head because when you've made the separate parts transparent you've done over the lines at the top of the head. You should try using the reference sheets in the preset folder to make sure you are only removing what you want to remove. Also, thats the same with the bottom jaw, you need to make sure you're only removing what you want too.Seconly, to remove the teeth and the eyes you need to make the whole set teeth and eyes need to be made transparent. if you are, make sure you've got the right coding in your preset file, and make sure that the file name has .png at the end.
You need to make a transparent image for your eyes not delete the eye section in the coding.