Raen, at times like this I realize just how poorly I chose my nickname here.
What goes from one person to the other is the DIRECT object. The $50.
The person who receives the direct object is the INDIRECT object. The clerk.
I sent a letter to my sister. The letter is the DO, and my sister is the IO.
"exactly how that was done" is, I think a noun phrase serving as the object. Exactly what was done is what I'd like to know. See how it serves as the subject when you turn it around? It's a noun phrase.
I'm sorry, but someone else is going to have to address your second question. I've never seen the value in learning this stuff. I tell my 11 year old that, but then tell her she has to do her homework anyway.