The eyes are actually just a rendered picture, I was trying to go for something barely visible, trying to be creepy in a subtle way, but the limitations of rpgm2003 plus my inexperience with the engine got in the way a bit. I'm glad you liked it though :)
For some short context, this was originally inspired by a specific "entity" in BloodBorne (for lack of a better word, and to avoid spoilers) that freaked me out back in the day. Now that I think about it, this whole segment is quite similar in more ways that one, I hadn't even realized it.
If you are having troubles on that specific area, and at the risk of doing some backseating on my end, there isn't a specific order on how to proceed through the game, so feel free to explore other parts of the world
Thanks for the comment!