I really need help hooking up 36 8x8 matrix! I have no idea where to start can someone please help!!
You are going to have to provide much more information than this. Are they just an LED matrix or are there any drivers with them.
There are too many to control in software from an arduino so you need to get some hardware help in the form of a scanning driver.
This is going to be very expensive, and is not something you can tackle as a first project.