The only part I'm not clear about is once the SOQ is complete, do you remove the bold fonts above the body paragraphs? In particularly with one SOQ that I did they asked to place the number next to the paragraph so they know which question it refers to that I was responding to.

This is a good basic example that hasn't been seen before on KZfaq. The SOQ's can vary from agency to agency and position to position. Sometimes they have two questions and other times they'll have three separate questions. Also I've seen the ones that just say tell us why you believe you're the most qualified for this position by stating your experience and education. That last one I find is the easiest one.