It's pretty simple
You just put one small string of text where you want the banner(s) to appear.
I have a rotation of small ones in the header ad location 1, primary banners on top and bottom of each page, and a general banner every 5th post. (all are managed by this great tool)
It provides statistics for each banner, and a link someone can click remotely to check it in realtime.
I have been using it at
www.ppfacorner.com for over 3 years now.