You can create banner ads that appear at the top of the Menu pane, within lengthy lists (i.e. of sessions, speakers, attendees, companies, etc.), and at the end of those modules. You can upload as many as you like and they will rotate in a random order every time you click into another page or section.
You can also put all of your banner ads into a GIF file so they rotate at a rate and in an order determined by you. Keep in mind that, if you make a GIF, it has to be exactly 50 pixels high and 300 pixels wide. If you crop the image, the system will convert it to a JPEG and it will lose its animation.
However, if you would prefer to keep a section ad-free, you can opt not to have them appear there. To deselect sections, just navigate to the Ad Settings tab of your Banner Ads module and uncheck them. This will prevent banner ads in general from showing in these sections; at this time, you cannot customize the placement of specific banner ads.
You can find more information on banner ads in this article of the FAQs.