This is not my idea, but I've begun using it in my setup.
A fishing reel with some heavy line and some type of latch on the end works great for both aligning your flags as well as keeping them at a proper height.
I attach the line to the bench (I've seen some use the front leg of their rest) and walk the reel out to the target board/frame and wrap it around from the bottom.
I then set my flags up along the line, using the line as my max height. You can experiment with the line running from the right side of the bench to the left side of the target frame, or vice versa, to get a sort of angular view of your flags.
Most people I see using a windicator have it sort of close to the bench, but I've also seen folks have several positioned downrange in conjuction with their flags. I have 2 medium sized orlando windicators and like to keep one up close to the bench and the other somewhere just past midrange, but that's me. You should experiment to see where it works best for your range and your eyes.
In my very short career, I've learned flags and windicators, and their placement is very personal. Most seem to place them at some sort of equal distance, but some may have more uprange or downrange depending on the range and their eyes.