"Send over" is used when the object is traveling over a distance, and that object is being brought by a person. For example, imagine that the electricity to your house goes out, and you need a flashlight, but don't have one. You call your neighbor to ask if you can borrow their's. Your neighbor tells you, "Sure, I will send my son over with it."
You use "send through" when the object has to cross some type of barrier in order to get to you. As an example of this, if your boss or secretary has a call on hold for you you would say "Send the call through." In this case, you boss or secretary acted as a "barrier" to the call and it had to stop so that it could be allowed to get to its destination (you).
This might be unclear, if it is, please ask me to clarify more.