Router table: bit positioning and guard?
Number 1 and 2 are one in the same, adjust the fence to achieve the final product look. Example: total round over is 1/2" then move your fence to 1/2" from the bit. You start with the bit setup to cut 1/8" and pass your stock through. Raise it another 1/8" and repeat, continue until you achieve the desired end look. If you are doing a dado in a piece of stock, then you adjust your fence to accommodate the spacing for the dado slot, again adjusting the bit up 1/8" each pass and running the stock through until desired depth.

Number 3, well that is a safety guard, some people remove it if it interferes with the thickness of stock being routed. Others remove it just to have it out of the way. However, it is designed to pop up as you push your stock through the table and over the bit. This will keep most of the dust and debris in that part of the table instead of all over you, in your face, eyes, nose, etc....

Now that that is said. Most people don't bother with the 1/8" cut per pass, rather they set it to the depth of the final pass and just go for it, especially when you are doing multiple pieces of stock and want them to match. Imagine just being a 1/16" off from one to another, may not be noticeable at first glance, but up close...you will notice.