Everyone designs missions in a different way. If your method works and gets the results that you are hoping for, I know that others will enjoy them. No one who toils in Mission Builder uses the same methods.
I tend to make mine overly complex, while other greats like Skylane, Ajax, Pen32Win, Talon, Cody Coyote, Shadow Wolf 07, and others all have their own methods. I'm sure we could all give advice that could get you turned around six ways from Sunday by the time we are finished.
The bottom line is...if it works and gets you the results you want, take the ball and run with it.